# DREME 5.3.3
#     command: dreme -oc ../result/final_prediction/GM12878/inference_raw/DREME/RankLinear1.0_10_CHD2/ -k 8 -m 5 -e 1000 -verbosity 1 -p ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/CHD2.fasta
#   positives: 250 from ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/CHD2.fasta (Sat Feb 12 17:35:45 EST 2022)
#   negatives: 250 from shuffled positives
#        host: c22n05.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 0.169 C 0.334 G 0.322 T 0.175


MOTIF CGCGAGAD DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CGCGAGAD   HTCTCGCG         47          4   1.6e-011   4.2e-008
#         CGCGAGAA   TTCTCGCG         20          1   7.3e-006   1.9e-002
#         CGCGAGAT   ATCTCGCG         13          0   1.0e-004   2.7e-001
#         CGCGAGAG   CTCTCGCG         15          3   3.3e-003   8.5e+000

letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 4.2e-008
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
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.404255 0.000000 0.319149 0.276596


MOTIF GATCCCGC DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    GATCCCGC   GCGGGATC          5          0   3.1e-002   7.4e+001

letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 7.4e+001
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
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000


MOTIF GCGCGGGA DREME-3

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

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


MOTIF TATCGCGA DREME-4

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

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


MOTIF CCCTCCCC DREME-5

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CCCTCCCC   GGGGAGGG          5          1   1.1e-001   2.5e+002

letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 2.5e+002
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 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 1.000000 0.000000 0.000000


# Stopping reason: target motif count reached
#    Running time: 0.64 seconds