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MEME - Motif discovery tool
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MEME version 5.5.0 (Release date: Wed Sep 7 14:18:26 2022 -0700)
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= betacor.fa
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
orf1ab 1.0000 212 NS2a 1.0000 100
HE 1.0000 100 S 1.0000 100
NS4 1.0000 100 NS5 1.0000 100
E 1.0000 100 M 1.0000 100
N2 1.0000 100 N 1.0000 100
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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 betacor.fa -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 6 -maxw 10 -objfun classic -markov_order 0
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= 10
nsites: minsites= 2 maxsites= 10 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= 1112 N= 10
sample: seed= 0 hsfrac= 0
searchsize= 1112 norand= no csites= 1000
Letter frequencies in dataset:
A 0.305 C 0.194 G 0.199 T 0.302
Background letter frequencies (from file dataset with add-one prior applied):
A 0.305 C 0.194 G 0.199 T 0.302
Background model order: 0
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MOTIF TMATCTAAAM MEME-1 width = 10 sites = 7 llr = 71 E-value = 4.8e-001
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Motif TMATCTAAAM MEME-1 Description
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Simplified A :67:::7a94
pos.-specific C :43:a:3:16
probability G ::::::::::
matrix T a::a:a::::
bits 2.4 *
2.1 *
1.9 *
1.7 * *** *
Relative 1.4 * *** *
Entropy 1.2 * *** ***
(14.7 bits) 0.9 **********
0.7 **********
0.5 **********
0.2 **********
0.0 ----------
Multilevel TAATCTAAAC
consensus CC C A
sequence
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Motif TMATCTAAAM MEME-1 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- ----------
M 88 1.74e-06 GATGTCTAGT TCATCTAAAC ATT
S 91 4.48e-06 CGTAGGCCAT TAATCTAAAC
NS2a 87 4.48e-06 TAAATGTTAG TAATCTAAAC TAAA
orf1ab 59 4.48e-06 AGATCTAATC TAATCTAAAC TTTATAAAAA
N 38 3.19e-05 CCGGCTGCCA TCCTCTCAAA AAGGGAATGG
N2 55 3.19e-05 CCGGCTGCCA TCCTCTCAAA AAGGGAATGG
NS4 85 4.22e-05 GCAGAGCCCG TAATCTAACA TTCACA
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Motif TMATCTAAAM MEME-1 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
M 1.7e-06 87_[+1]_3
S 4.5e-06 90_[+1]
NS2a 4.5e-06 86_[+1]_4
orf1ab 4.5e-06 58_[+1]_144
N 3.2e-05 37_[+1]_53
N2 3.2e-05 54_[+1]_36
NS4 4.2e-05 84_[+1]_6
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Motif TMATCTAAAM MEME-1 in BLOCKS format
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BL MOTIF TMATCTAAAM width=10 seqs=7
M ( 88) TCATCTAAAC 1
S ( 91) TAATCTAAAC 1
NS2a ( 87) TAATCTAAAC 1
orf1ab ( 59) TAATCTAAAC 1
N ( 38) TCCTCTCAAA 1
N2 ( 55) TCCTCTCAAA 1
NS4 ( 85) TAATCTAACA 1
//
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Motif TMATCTAAAM MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 10 n= 1022 bayes= 7.78904 E= 4.8e-001
-945 -945 -945 172
91 114 -945 -945
123 56 -945 -945
-945 -945 -945 172
-945 236 -945 -945
-945 -945 -945 172
123 56 -945 -945
171 -945 -945 -945
149 -44 -945 -945
49 156 -945 -945
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Motif TMATCTAAAM MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 10 nsites= 7 E= 4.8e-001
0.000000 0.000000 0.000000 1.000000
0.571429 0.428571 0.000000 0.000000
0.714286 0.285714 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
0.714286 0.285714 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.857143 0.142857 0.000000 0.000000
0.428571 0.571429 0.000000 0.000000
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Motif TMATCTAAAM MEME-1 regular expression
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T[AC][AC]TCT[AC]AA[CA]
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Time 0.34 secs.
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MOTIF CCGGCTGCC MEME-2 width = 9 sites = 2 llr = 28 E-value = 4.3e+001
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Motif CCGGCTGCC MEME-2 Description
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Simplified A :::::::::
pos.-specific C aa::a::aa
probability G ::aa::a::
matrix T :::::a:::
bits 2.4 ***** ***
2.1 ***** ***
1.9 ***** ***
1.7 *********
Relative 1.4 *********
Entropy 1.2 *********
(20.5 bits) 0.9 *********
0.7 *********
0.5 *********
0.2 *********
0.0 ---------
Multilevel CCGGCTGCC
consensus
sequence
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Motif CCGGCTGCC MEME-2 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- ---------
N 28 6.54e-07 TCGGCAATTA CCGGCTGCC ATCCTCTCAA
N2 45 6.54e-07 TCGGCAATTA CCGGCTGCC ATCCTCTCAA
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Motif CCGGCTGCC MEME-2 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
N 6.5e-07 27_[+2]_64
N2 6.5e-07 44_[+2]_47
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Motif CCGGCTGCC MEME-2 in BLOCKS format
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BL MOTIF CCGGCTGCC width=9 seqs=2
N ( 28) CCGGCTGCC 1
N2 ( 45) CCGGCTGCC 1
//
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Motif CCGGCTGCC MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 9 n= 1032 bayes= 9.00843 E= 4.3e+001
-765 236 -765 -765
-765 236 -765 -765
-765 -765 233 -765
-765 -765 233 -765
-765 236 -765 -765
-765 -765 -765 172
-765 -765 233 -765
-765 236 -765 -765
-765 236 -765 -765
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Motif CCGGCTGCC MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 9 nsites= 2 E= 4.3e+001
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 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 1.000000 0.000000 0.000000
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Motif CCGGCTGCC MEME-2 regular expression
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CCGGCTGCC
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Time 0.65 secs.
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MOTIF TCGGCAATT MEME-3 width = 9 sites = 4 llr = 44 E-value = 1.6e+002
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Motif TCGGCAATT MEME-3 Description
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Simplified A :::::a8::
pos.-specific C :a::8:33:
probability G ::aa:::::
matrix T a:::3::8a
bits 2.4 ***
2.1 ***
1.9 ***
1.7 **** * *
Relative 1.4 ****** *
Entropy 1.2 *********
(15.7 bits) 0.9 *********
0.7 *********
0.5 *********
0.2 *********
0.0 ---------
Multilevel TCGGCAATT
consensus T CC
sequence
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Motif TCGGCAATT MEME-3 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- ---------
N 18 3.82e-06 AAGTCCAAAG TCGGCAATT ACCGGCTGCC
N2 35 3.82e-06 AAGTCCAAAG TCGGCAATT ACCGGCTGCC
NS5 65 1.03e-05 CTTATAATTT TCGGCACCT GCCGAAATTT
E 14 1.62e-05 TTTAAGAGCT TCGGTAATT CACCTTCCGA
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Motif TCGGCAATT MEME-3 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
N 3.8e-06 17_[+3]_74
N2 3.8e-06 34_[+3]_57
NS5 1e-05 64_[+3]_27
E 1.6e-05 13_[+3]_78
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Motif TCGGCAATT MEME-3 in BLOCKS format
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BL MOTIF TCGGCAATT width=9 seqs=4
N ( 18) TCGGCAATT 1
N2 ( 35) TCGGCAATT 1
NS5 ( 65) TCGGCACCT 1
E ( 14) TCGGTAATT 1
//
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Motif TCGGCAATT MEME-3 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 9 n= 1032 bayes= 8.00562 E= 1.6e+002
-865 -865 -865 172
-865 236 -865 -865
-865 -865 233 -865
-865 -865 233 -865
-865 195 -865 -27
171 -865 -865 -865
130 36 -865 -865
-865 36 -865 131
-865 -865 -865 172
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Motif TCGGCAATT MEME-3 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 9 nsites= 4 E= 1.6e+002
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 0.000000 1.000000 0.000000
0.000000 0.750000 0.000000 0.250000
1.000000 0.000000 0.000000 0.000000
0.750000 0.250000 0.000000 0.000000
0.000000 0.250000 0.000000 0.750000
0.000000 0.000000 0.000000 1.000000
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Motif TCGGCAATT MEME-3 regular expression
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TCGG[CT]A[AC][TC]T
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Time 0.96 secs.
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SUMMARY OF MOTIFS
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
orf1ab 1.38e-02 58_[+1(4.48e-06)]_144
NS2a 1.38e-02 86_[+1(4.48e-06)]_4
HE 6.97e-01 100
S 1.92e-03 90_[+1(4.48e-06)]
NS4 5.00e-02 84_[+1(4.22e-05)]_6
NS5 5.65e-03 64_[+3(1.03e-05)]_27
E 2.56e-02 13_[+3(1.62e-05)]_78
M 5.23e-03 87_[+1(1.74e-06)]_3
N2 1.85e-08 34_[+3(3.82e-06)]_1_[+2(6.54e-07)]_\
1_[+1(3.19e-05)]_36
N 1.85e-08 17_[+3(3.82e-06)]_1_[+2(6.54e-07)]_\
1_[+1(3.19e-05)]_53
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Stopped because requested number of motifs (3) found.
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CPU: noble-meme.grid.gs.washington.edu
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