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********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000)
For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme-suite.org .
This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs. MAST is available
for interactive use and downloading at http://meme-suite.org .
********************************************************************************
********************************************************************************
REFERENCE
********************************************************************************
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.
********************************************************************************
********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= rna_samples.fa
ALPHABET= ACGU
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
ce1cg 1.0000 105 ara 1.0000 105
bglr1 1.0000 105 crp 1.0000 105
cya 1.0000 105 deop2 1.0000 105
gale 1.0000 105
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme rna_samples.fa -nmotifs 2 -rna -mod oops
model: mod= oops nmotifs= 2 evt= inf
object function= E-value of product of p-values
width: minw= 8 maxw= 50
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 7 maxsites= 7 wnsites= 0.8
theta: spmap= uni spfuzz= 0.5
global: substring= yes branching= no wbranch= no
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 735 N= 7 shuffle= -1
sample: seed= 0 ctfrac= -1 maxwords= -1
Letter frequencies in dataset:
A 0.313 C 0.174 G 0.190 U 0.322
Background letter frequencies (from dataset with add-one prior applied):
A 0.313 C 0.175 G 0.191 U 0.322
********************************************************************************
********************************************************************************
MOTIF 1 MEME width = 19 sites = 7 llr = 97 E-value = 7.2e-003
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :::364:14:1::91a116
pos.-specific C ::1:1:93:4::9:7:4::
probability G :3:6:116137:11:::::
matrix U a79134::431a::1:494
bits 2.5
2.3
2.0 * *
1.8 * * *
Relative 1.5 * * ** *
Entropy 1.3 * * * *** *
(19.9 bits) 1.0 *** ** ****** *
0.8 **** ** ******* **
0.5 ***** ** **********
0.3 *******************
0.0 -------------------
Multilevel UUUGAACGACGUCACACUA
consensus G AUU CUG U U
sequence U
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- -------------------
ara 58 1.37e-09 ACAUUGAUUA UUUGCACGGCGUCACACUU UGCUAUGCCA
gale 45 3.90e-08 AUUCCACUAA UUUAUUCCAUGUCACACUU UUCGCAUCUU
deop2 10 1.66e-07 AGUGAAUUA UUUGAACCAGAUCGCAUUA CAGUGAUGCA
crp 66 2.14e-07 ACUGCAUGUA UGCAAAGGACGUCACAUUA CCGUGCAGUA
bglr1 79 6.30e-07 AGUUAAUAAC UGUGAGCAUGGUCAUAUUU UUAUCAAU
ce1cg 64 6.75e-07 AGACUGUUUU UUUGAUCGUUUUCACAAAA AUGGAAGUCC
cya 79 7.76e-07 UUUUAGACCA UUUUUUCGUCGUGAAACUA AAAAAACC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
ara 1.4e-09 57_[1]_29
gale 3.9e-08 44_[1]_42
deop2 1.7e-07 9_[1]_77
crp 2.1e-07 65_[1]_21
bglr1 6.3e-07 78_[1]_8
ce1cg 6.8e-07 63_[1]_23
cya 7.8e-07 78_[1]_8
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=19 seqs=7
ara ( 58) UUUGCACGGCGUCACACUU 1
gale ( 45) UUUAUUCCAUGUCACACUU 1
deop2 ( 10) UUUGAACCAGAUCGCAUUA 1
crp ( 66) UGCAAAGGACGUCACAUUA 1
bglr1 ( 79) UGUGAGCAUGGUCAUAUUU 1
ce1cg ( 64) UUUGAUCGUUUUCACAAAA 1
cya ( 79) UUUUUUCGUCGUGAAACUA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 19 n= 609 bayes= 6.42626 E= 7.2e-003
-945 -945 -945 163
-945 -945 58 115
-945 -29 -945 141
-13 -945 158 -117
87 -29 -945 -17
45 -945 -42 41
-945 229 -42 -945
-113 71 158 -945
45 -945 -42 41
-945 129 58 -17
-113 -945 190 -117
-945 -945 -945 163
-945 229 -42 -945
145 -945 -42 -945
-113 203 -945 -117
168 -945 -945 -945
-113 129 -945 41
-113 -945 -945 141
87 -945 -945 41
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 19 nsites= 7 E= 7.2e-003
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.285714 0.714286
0.000000 0.142857 0.000000 0.857143
0.285714 0.000000 0.571429 0.142857
0.571429 0.142857 0.000000 0.285714
0.428571 0.000000 0.142857 0.428571
0.000000 0.857143 0.142857 0.000000
0.142857 0.285714 0.571429 0.000000
0.428571 0.000000 0.142857 0.428571
0.000000 0.428571 0.285714 0.285714
0.142857 0.000000 0.714286 0.142857
0.000000 0.000000 0.000000 1.000000
0.000000 0.857143 0.142857 0.000000
0.857143 0.000000 0.142857 0.000000
0.142857 0.714286 0.000000 0.142857
1.000000 0.000000 0.000000 0.000000
0.142857 0.428571 0.000000 0.428571
0.142857 0.000000 0.000000 0.857143
0.571429 0.000000 0.000000 0.428571
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
U[UG]U[GA][AU][AU]C[GC][AU][CGU]GUCACA[CU]U[AU]
--------------------------------------------------------------------------------
Time 0.13 secs.
********************************************************************************
********************************************************************************
MOTIF 2 MEME width = 9 sites = 7 llr = 54 E-value = 7.6e+002
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 11:6:::1a
pos.-specific C :4::::71:
probability G 9:43:a:1:
matrix U :461a:36:
bits 2.5
2.3 *
2.0 *
1.8 * * *
Relative 1.5 * *** *
Entropy 1.3 * *** *
(11.1 bits) 1.0 * * *** *
0.8 * * *** *
0.5 ******* *
0.3 *********
0.0 ---------
Multilevel GCUAUGCUA
consensus UGG U
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- ---------
crp 13 7.14e-06 CAAAGCGAAA GCUAUGCUA AAACAGUCAG
gale 75 2.50e-05 UCGCAUCUUU GUUAUGCUA UGGUUAUUUC
ara 78 3.26e-05 GUCACACUUU GCUAUGCCA UAGCAUUUUU
deop2 31 1.10e-04 UCGCAUUACA GUGAUGCAA ACUUGUAAGU
cya 1 1.73e-04 . ACGGUGCUA CACUUGUAUG
ce1cg 44 3.33e-04 AGAAUAGCGC GUGGUGUGA AAGACUGUUU
bglr1 27 8.67e-04 UAAUUAUUGG GAUUUGUUA UAUAUAACUU
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
crp 7.1e-06 12_[2]_84
gale 2.5e-05 74_[2]_22
ara 3.3e-05 77_[2]_19
deop2 0.00011 30_[2]_66
cya 0.00017 [2]_96
ce1cg 0.00033 43_[2]_53
bglr1 0.00087 26_[2]_70
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=9 seqs=7
crp ( 13) GCUAUGCUA 1
gale ( 75) GUUAUGCUA 1
ara ( 78) GCUAUGCCA 1
deop2 ( 31) GUGAUGCAA 1
cya ( 1) ACGGUGCUA 1
ce1cg ( 44) GUGGUGUGA 1
bglr1 ( 27) GAUUUGUUA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 9 n= 679 bayes= 6.58496 E= 7.6e+002
-113 -945 217 -945
-113 129 -945 41
-945 -945 117 83
87 -945 58 -117
-945 -945 -945 163
-945 -945 239 -945
-945 203 -945 -17
-113 -29 -42 83
168 -945 -945 -945
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 9 nsites= 7 E= 7.6e+002
0.142857 0.000000 0.857143 0.000000
0.142857 0.428571 0.000000 0.428571
0.000000 0.000000 0.428571 0.571429
0.571429 0.000000 0.285714 0.142857
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.714286 0.000000 0.285714
0.142857 0.142857 0.142857 0.571429
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
G[CU][UG][AG]UG[CU]UA
--------------------------------------------------------------------------------
Time 0.17 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
ce1cg 2.65e-05 63_[1(6.75e-07)]_23
ara 8.53e-09 57_[1(1.37e-09)]_1_[2(3.26e-05)]_19
bglr1 5.90e-05 78_[1(6.30e-07)]_8
crp 2.47e-07 12_[2(7.14e-06)]_44_[1(2.14e-07)]_\
21
cya 1.65e-05 78_[1(7.76e-07)]_8
deop2 2.56e-06 9_[1(1.66e-07)]_77
gale 1.61e-07 44_[1(3.90e-08)]_11_[2(2.50e-05)]_\
22
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because requested number of motifs (2) found.
********************************************************************************
CPU: pc
********************************************************************************
|
