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MEME - Motif discovery tool
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MEME version 5.5.2 (Release date: Sun Jan 29 10:33:12 2023 -0800)
For further information on how to interpret these results please access https://meme-suite.org/meme.
To get a copy of the MEME Suite software please access https://meme-suite.org.
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REFERENCE
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If you use this program in your research, please cite:
Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to
discover motifs in biopolymers",
Proceedings of the Second International Conference on Intelligent Systems
for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
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TRAINING SET
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PRIMARY SEQUENCES= GSM6180992-S1_END_seq_SW48_replicate2_meme-chip/seqs-centered
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
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COMMAND LINE SUMMARY
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This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme GSM6180992-S1_END_seq_SW48_replicate2_meme-chip/seqs-centered -oc GSM6180992-S1_END_seq_SW48_replicate2_meme-chip/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 15 -bfile GSM6180992-S1_END_seq_SW48_replicate2_meme-chip/background -dna -searchsize 100000 -revcomp -nostatus -mpi
model: mod= zoops nmotifs= 3 evt= inf
objective function: em= E-value of product of p-values
starts= E-value of product of p-values
strands: + -
width: minw= 6 maxw= 15
nsites: minsites= 2 maxsites= 2000 wnsites= 0.8
theta: spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
trim: wg= 11 ws= 1 endgaps= yes
data: n= 200000 N= 2000
sample: seed= 0 hsfrac= 0
searchsize= 100000 norand= no csites= 1000
Letter frequencies in dataset:
A 0.367 C 0.133 G 0.133 T 0.367
Background letter frequencies (from file GSM6180992-S1_END_seq_SW48_replicate2_meme-chip/background):
A 0.328 C 0.172 G 0.172 T 0.328
Background model order: 2
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MOTIF ATATATATATA MEME-1 width = 11 sites = 1556 llr = 19010 E-value = 3.2e-2088
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Motif ATATATATATA MEME-1 Description
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Simplified A a:a:a:a:a:a
pos.-specific C :::::::::::
probability G :::::::::::
matrix T :a:a:a:a:a:
bits 2.5
2.3
2.0
1.8
Relative 1.5 ***********
Entropy 1.3 ***********
(17.6 bits) 1.0 ***********
0.8 ***********
0.5 ***********
0.3 ***********
0.0 -----------
Multilevel ATATATATATA
consensus
sequence
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Motif ATATATATATA MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 11 n= 180000 bayes= 7.95839 E= 3.2e-2088
161 -1725 -1725 -1725
-1725 -1725 -807 161
161 -1725 -807 -1725
-899 -1725 -1725 161
161 -1725 -1725 -1725
-899 -1725 -1725 161
161 -1725 -1725 -1725
-1725 -1725 -1725 161
161 -1725 -607 -899
-799 -1725 -1725 161
161 -1725 -1725 -799
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Motif ATATATATATA MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 11 nsites= 1556 E= 3.2e-2088
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000643 0.999357
0.999357 0.000000 0.000643 0.000000
0.000643 0.000000 0.000000 0.999357
1.000000 0.000000 0.000000 0.000000
0.000643 0.000000 0.000000 0.999357
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.996787 0.000000 0.002571 0.000643
0.001285 0.000000 0.000000 0.998715
0.998715 0.000000 0.000000 0.001285
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Motif ATATATATATA MEME-1 regular expression
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ATATATATATA
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Time 20.40 secs.
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MOTIF CTYTCTYTCTYTCTY MEME-2 width = 15 sites = 471 llr = 7019 E-value = 8.5e-712
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Motif CTYTCTYTCTYTCTY MEME-2 Description
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Simplified A :::::::::::::::
pos.-specific C 9:429141a:42a:5
probability G :::::::::::::::
matrix T 1a681969:a68:a5
bits 2.5
2.3 * *
2.0 * * *
1.8 * * * *
Relative 1.5 ** * ** *
Entropy 1.3 ** ** *** **
(21.5 bits) 1.0 ***************
0.8 ***************
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel CTTTCTTTCTTTCTC
consensus C C C T
sequence
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Motif CTYTCTYTCTYTCTY MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 10.2069 E= 8.5e-712
-726 243 -1552 -231
-726 -1552 -1552 161
-1552 135 -1552 78
-1552 1 -1552 133
-410 231 -1552 -139
-1552 -59 -1552 143
-1552 136 -1552 76
-568 -73 -1552 144
-726 251 -334 -1552
-726 -288 -1552 157
-1552 123 -402 84
-627 7 -1552 132
-726 249 -1552 -346
-627 -217 -1552 155
-627 161 -634 51
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Motif CTYTCTYTCTYTCTY MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 15 nsites= 471 E= 8.5e-712
0.002123 0.932059 0.000000 0.065817
0.002123 0.000000 0.000000 0.997877
0.000000 0.439490 0.000000 0.560510
0.000000 0.174098 0.000000 0.825902
0.019108 0.855626 0.000000 0.125265
0.000000 0.114650 0.000000 0.885350
0.000000 0.443737 0.000000 0.556263
0.006369 0.104034 0.000000 0.889597
0.002123 0.980892 0.016985 0.000000
0.002123 0.023355 0.000000 0.974522
0.000000 0.403397 0.010616 0.585987
0.004246 0.180467 0.000000 0.815287
0.002123 0.968153 0.000000 0.029724
0.004246 0.038217 0.000000 0.957537
0.004246 0.526539 0.002123 0.467091
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Motif CTYTCTYTCTYTCTY MEME-2 regular expression
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CT[TC]TCT[TC]TCT[TC]TCT[CT]
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Time 36.15 secs.
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MOTIF TCTYTCTYTCTYTCY MEME-3 width = 15 sites = 533 llr = 6923 E-value = 2.9e-595
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Motif TCTYTCTYTCTYTCY MEME-3 Description
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Simplified A ::::1:::::::1::
pos.-specific C :a241925:824:94
probability G ::::1::::2::1::
matrix T a:867185a:86816
bits 2.5
2.3 *
2.0 * *
1.8 * * *
Relative 1.5 * * ** *
Entropy 1.3 ** * ** *
(18.7 bits) 1.0 **** ** **** **
0.8 **** **********
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel TCTTTCTTTCTTTCT
consensus C C CC C
sequence
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Motif TCTYTCTYTCTYTCY MEME-3 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 9.68294 E= 2.9e-595
-512 -244 -1570 155
-545 246 -1570 -299
-645 -11 -1570 135
-744 122 -652 86
-178 -106 -97 116
-512 244 -652 -264
-586 14 -1570 130
-545 148 -262 56
-744 -652 -1570 160
-428 216 6 -345
-445 25 -1570 125
-1570 115 -1570 91
-206 -262 -79 128
-545 239 -272 -240
-744 132 -652 79
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Motif TCTYTCTYTCTYTCY MEME-3 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 15 nsites= 533 E= 2.9e-595
0.009381 0.031895 0.000000 0.958724
0.007505 0.951220 0.000000 0.041276
0.003752 0.159475 0.000000 0.836773
0.001876 0.401501 0.001876 0.594747
0.095685 0.082552 0.088180 0.733583
0.009381 0.936210 0.001876 0.052533
0.005629 0.189493 0.000000 0.804878
0.007505 0.480300 0.028143 0.484053
0.001876 0.001876 0.000000 0.996248
0.016886 0.772983 0.180113 0.030019
0.015009 0.204503 0.000000 0.780488
0.000000 0.382739 0.000000 0.617261
0.078799 0.028143 0.099437 0.793621
0.007505 0.904315 0.026266 0.061914
0.001876 0.431520 0.001876 0.564728
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Motif TCTYTCTYTCTYTCY MEME-3 regular expression
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TCT[TC]TCT[TC]TC[TC][TC]TC[TC]
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Time 51.11 secs.
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Stopped because requested number of motifs (3) found.
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CPU: snode015.sibcb.ac.cn
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