# DREME 5.3.3
#     command: dreme -oc ../result/final_prediction/GM12878/inference_raw/DREME/RankLinear1.0_10_CTCF/ -k 8 -m 5 -e 1000 -verbosity 1 -p ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/CTCF.fasta
#   positives: 250 from ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/CTCF.fasta (Sat Feb 12 17:35:52 EST 2022)
#   negatives: 250 from shuffled positives
#        host: c22n09.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 0.185 C 0.319 G 0.307 T 0.190


MOTIF CCACYAGR DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CCACYAGR   YCTRGTGG         55          4   4.7e-014   9.8e-011
#         CCACTAGG   CCTAGTGG         19          1   1.5e-005   3.1e-002
#         CCACCAGG   CCTGGTGG         13          1   8.0e-004   1.7e+000
#         CCACCAGA   TCTGGTGG         12          1   1.5e-003   3.2e+000
#         CCACTAGA   TCTAGTGG         11          1   2.9e-003   6.1e+000

letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 9.8e-011
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
0.000000 0.454545 0.000000 0.545455
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.418182 0.000000 0.581818 0.000000


MOTIF CCAGCAGR DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CCAGCAGR   YCTGCTGG         28          2   2.2e-007   4.1e-004
#         CCAGCAGA   TCTGCTGG         14          0   5.1e-005   9.6e-002
#         CCAGCAGG   CCTGCTGG         14          2   1.8e-003   3.4e+000

letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 4.1e-004
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 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
0.500000 0.000000 0.500000 0.000000


MOTIF AGGTGGCR DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    AGGTGGCR   YGCCACCT         24          2   3.2e-006   5.8e-003
#         AGGTGGCG   CGCCACCT         13          1   8.0e-004   1.5e+000
#         AGGTGGCA   TGCCACCT         11          1   2.9e-003   5.3e+000

letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 5.8e-003
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 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
0.458333 0.000000 0.541667 0.000000


MOTIF ACACTAGA DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    ACACTAGA   TCTAGTGT          5          0   3.1e-002   5.3e+001

letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 5.3e+001
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 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF AGAGGGCA DREME-5

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    AGAGGGCA   TGCCCTCT          5          0   3.1e-002   5.2e+001

letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 5.2e+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
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 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000


# Stopping reason: target motif count reached
#    Running time: 0.62 seconds