# DREME 5.3.3
#     command: dreme -oc ../result/final_prediction/GM12878/inference_raw/DREME/RankLinear1.0_10_BRCA1/ -k 8 -m 5 -e 1000 -verbosity 1 -p ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/BRCA1.fasta
#   positives: 250 from ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/BRCA1.fasta (Sat Feb 12 17:35:27 EST 2022)
#   negatives: 250 from shuffled positives
#        host: c22n08.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 0.176 C 0.325 G 0.324 T 0.175


MOTIF BTCTCGCG DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    BTCTCGCG   CGCGAGAV         46          3   4.7e-012   1.2e-008
#         CTCTCGCG   CGCGAGAG         21          2   2.3e-005   5.9e-002
#         GTCTCGCG   CGCGAGAC         17          1   5.6e-005   1.5e-001
#         TTCTCGCG   CGCGAGAA         13          0   1.0e-004   2.7e-001

letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 1.2e-008
0.000000 0.391304 0.347826 0.260870
0.000000 0.000000 0.000000 1.000000
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 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000


MOTIF CAGCGCCG DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CAGCGCCG   CGGCGCTG          4          0   6.2e-002   1.5e+002

letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.5e+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 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


MOTIF CGCGGGAG DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CGCGGGAG   CTCCCGCG          4          0   6.2e-002   1.5e+002

letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.5e+002
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
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000


MOTIF CTCACGAG DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CTCACGAG   CTCGTGAG          4          0   6.2e-002   1.5e+002

letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.5e+002
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
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
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000


MOTIF GAGATCCC DREME-5

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

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


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