# DREME 5.3.3
#     command: dreme -oc ../result/final_prediction/GM12878/inference_raw/DREME/RankLinear1.0_10_RAD51/ -k 8 -m 5 -e 1000 -verbosity 1 -p ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/RAD51.fasta
#   positives: 250 from ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/RAD51.fasta (Sat Feb 12 17:37:15 EST 2022)
#   negatives: 250 from shuffled positives
#        host: c22n07.farnam.hpc.yale.internal
#        when: Sat Feb 12 18:29:51 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 0.245 C 0.250 G 0.258 T 0.247


MOTIF CAYGTGAC DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CAYGTGAC   GTCACRTG         37          0   1.7e-012   4.6e-009
#         CACGTGAC   GTCACGTG         25          0   1.6e-008   4.2e-005
#         CATGTGAC   GTCACATG         13          0   1.0e-004   2.8e-001

letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 4.6e-009
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.641026 0.000000 0.358974
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000


MOTIF ACAGGGGG DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    ACAGGGGG   CCCCCTGT          9          0   1.8e-003   4.5e+000
#         ACAGGGGG   CCCCCTGT          9          0   1.8e-003   4.5e+000

letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 4.5e+000
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 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 0.000000 1.000000 0.000000


MOTIF ATCACGTG DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    ATCACGTG   CACGTGAT          8          0   3.7e-003   9.1e+000
#         ATCACGTG   CACGTGAT          8          0   3.7e-003   9.1e+000

letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 9.1e+000
1.000000 0.000000 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
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000


MOTIF CACATGAC DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CACATGAC   GTCATGTG          5          1   1.1e-001   2.6e+002

letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 2.6e+002
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 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000


MOTIF AAAGTCAG DREME-5

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    AAAGTCAG   CTGACTTT          3          0   1.2e-001   3.0e+002

letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 3.0e+002
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
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 0.000000 1.000000 0.000000


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