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********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.0 (Release date: 2001/03/05 14:24:28)
For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.sdsc.edu.
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.sdsc.edu.
********************************************************************************
********************************************************************************
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= D10Mit194.set.genbank.fasta.nref
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
20218 1.0000 2000 10657 1.0000 2000
83796 1.0000 2000 6603 1.0000 2000
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme D10Mit194.set.genbank.fasta.nref -dna -print_fasta -nmotifs 3 -maxw 25
model: mod= zoops nmotifs= 3 evt= inf
object function= E-value of product of p-values
width: minw= 8 maxw= 25 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 2 maxsites= 4 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 8000 N= 4
strands: +
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.255 C 0.236 G 0.252 T 0.257
Background letter frequencies (from dataset with add-one prior applied):
A 0.255 C 0.236 G 0.252 T 0.257
********************************************************************************
********************************************************************************
MOTIF 1 width = 25 sites = 4 llr = 106 E-value = 1.2e-002
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :8:88aaa:53a8:::3:a::3::3
pos.-specific C a3::3:::::3:::5a8a:8a5aa8
probability G ::8:::::3:5::::::::3:::::
matrix T ::33::::85::3a5::::::3:::
bits 2.1 * * * * **
1.9 * *** * * * ** * **
1.7 * *** * * * ** * **
1.5 * *** * * * ** * **
Information 1.2 ********* *** ****** ***
content 1.0 ********** ********** ***
(38.1 bits) 0.8 ********** ********** ***
0.6 ********** **************
0.4 *************************
0.2 *************************
0.0 -------------------------
Multilevel CAGAAAAATAGAATCCCCACCCCCC
consensus CTTC GTA T T A G A A
sequence C T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- -------------------------
6603 1311 2.59e-15 GGCGCATTGA CAGAAAAATTGAATTCCCACCCCCC AATGAGGAGG
83796 1284 2.59e-15 GGAGGATTGA CAGAAAAATTGAATTCCCACCCCCC AACGAGGAGG
20218 938 6.34e-12 TTTTTGGTAA CCTTAAAATAAAATCCCCACCACCA CTTTTAAAAA
10657 1685 8.70e-12 GGCCCGCGCG CAGACAAAGACATTCCACAGCTCCC GCCCCCTCCA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
6603 2.6e-15 1310_[1]_665
83796 2.6e-15 1283_[1]_692
20218 6.3e-12 937_[1]_1038
10657 8.7e-12 1684_[1]_291
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in FASTA format
--------------------------------------------------------------------------------
>6603 pos 1311
CAGAAAAATTGAATTCCCACCCCCC
>83796 pos 1284
CAGAAAAATTGAATTCCCACCCCCC
>20218 pos 938
CCTTAAAATAAAATCCCCACCACCA
>10657 pos 1685
CAGACAAAGACATTCCACAGCTCCC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 11.6849 E= 1.2e-002
-865 208 -865 -865
156 8 -865 -865
-865 -865 157 -4
156 -865 -865 -4
156 8 -865 -865
197 -865 -865 -865
197 -865 -865 -865
197 -865 -865 -865
-865 -865 -1 154
97 -865 -865 96
-3 8 99 -865
197 -865 -865 -865
156 -865 -865 -4
-865 -865 -865 196
-865 108 -865 96
-865 208 -865 -865
-3 166 -865 -865
-865 208 -865 -865
197 -865 -865 -865
-865 166 -1 -865
-865 208 -865 -865
-3 108 -865 -4
-865 208 -865 -865
-865 208 -865 -865
-3 166 -865 -865
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 25 n= 7904 E= 1.2e-002
0.000635 0.998096 0.000629 0.000640
0.748765 0.249966 0.000629 0.000640
0.000635 0.000589 0.748759 0.250017
0.748765 0.000589 0.000629 0.250017
0.748765 0.249966 0.000629 0.000640
0.998141 0.000589 0.000629 0.000640
0.998141 0.000589 0.000629 0.000640
0.998141 0.000589 0.000629 0.000640
0.000635 0.000589 0.250006 0.748770
0.499388 0.000589 0.000629 0.499393
0.250012 0.249966 0.499382 0.000640
0.998141 0.000589 0.000629 0.000640
0.748765 0.000589 0.000629 0.250017
0.000635 0.000589 0.000629 0.998147
0.000635 0.499343 0.000629 0.499393
0.000635 0.998096 0.000629 0.000640
0.250012 0.748719 0.000629 0.000640
0.000635 0.998096 0.000629 0.000640
0.998141 0.000589 0.000629 0.000640
0.000635 0.748719 0.250006 0.000640
0.000635 0.998096 0.000629 0.000640
0.250012 0.499343 0.000629 0.250017
0.000635 0.998096 0.000629 0.000640
0.000635 0.998096 0.000629 0.000640
0.250012 0.748719 0.000629 0.000640
--------------------------------------------------------------------------------
Time 38.44 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 25 sites = 4 llr = 101 E-value = 4.5e-001
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A ::::a::383:5:3:::a33:83:a
pos.-specific C a3a8:3a33:a::5::8::::383:
probability G ::::::::::::::::3:38a::8:
matrix T :8:3:8:5:8:5a3aa::5::::::
bits 2.1 * * * * *
1.9 * * * * * * ** * * *
1.7 * * * * * * ** * * *
1.5 * * * * * * ** * * *
Information 1.2 ******* *** * **** ******
content 1.0 ******* ***** **** ******
(36.6 bits) 0.8 ******* ***** **** ******
0.6 ******* ********** ******
0.4 *************************
0.2 *************************
0.0 -------------------------
Multilevel CTCCATCTATCATCTTCATGGACGA
consensus C T C ACA T A G AA CAC
sequence C T G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- -------------------------
6603 1000 1.62e-15 CGGGAACATG CTCCATCTATCATCTTCATGGACGA AATCGACTCC
83796 978 4.69e-15 CGAGAACATG CTCCATCCATCATCTTCATGGACGA GATTGACTCT
20218 1545 1.69e-11 TAGCTTCTCT CCCCATCAATCTTATTCAGAGCCCA CCCCTCCCCC
10657 1075 3.40e-11 AGGATCTGGT CTCTACCTCACTTTTTGAAGGAAGA AACACTTAAT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
6603 1.6e-15 999_[2]_976
83796 4.7e-15 977_[2]_998
20218 1.7e-11 1544_[2]_431
10657 3.4e-11 1074_[2]_901
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in FASTA format
--------------------------------------------------------------------------------
>6603 pos 1000
CTCCATCTATCATCTTCATGGACGA
>83796 pos 978
CTCCATCCATCATCTTCATGGACGA
>20218 pos 1545
CCCCATCAATCTTATTCAGAGCCCA
>10657 pos 1075
CTCTACCTCACTTTTTGAAGGAAGA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 10.9476 E= 4.5e-001
-865 208 -865 -865
-865 8 -865 154
-865 208 -865 -865
-865 166 -865 -4
197 -865 -865 -865
-865 8 -865 154
-865 208 -865 -865
-3 8 -865 96
156 8 -865 -865
-3 -865 -865 154
-865 208 -865 -865
97 -865 -865 96
-865 -865 -865 196
-3 108 -865 -4
-865 -865 -865 196
-865 -865 -865 196
-865 166 -1 -865
197 -865 -865 -865
-3 -865 -1 96
-3 -865 157 -865
-865 -865 198 -865
156 8 -865 -865
-3 166 -865 -865
-865 8 157 -865
197 -865 -865 -865
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 25 n= 7904 E= 4.5e-001
0.000635 0.998096 0.000629 0.000640
0.000635 0.249966 0.000629 0.748770
0.000635 0.998096 0.000629 0.000640
0.000635 0.748719 0.000629 0.250017
0.998141 0.000589 0.000629 0.000640
0.000635 0.249966 0.000629 0.748770
0.000635 0.998096 0.000629 0.000640
0.250012 0.249966 0.000629 0.499393
0.748765 0.249966 0.000629 0.000640
0.250012 0.000589 0.000629 0.748770
0.000635 0.998096 0.000629 0.000640
0.499388 0.000589 0.000629 0.499393
0.000635 0.000589 0.000629 0.998147
0.250012 0.499343 0.000629 0.250017
0.000635 0.000589 0.000629 0.998147
0.000635 0.000589 0.000629 0.998147
0.000635 0.748719 0.250006 0.000640
0.998141 0.000589 0.000629 0.000640
0.250012 0.000589 0.250006 0.499393
0.250012 0.000589 0.748759 0.000640
0.000635 0.000589 0.998135 0.000640
0.748765 0.249966 0.000629 0.000640
0.250012 0.748719 0.000629 0.000640
0.000635 0.249966 0.748759 0.000640
0.998141 0.000589 0.000629 0.000640
--------------------------------------------------------------------------------
Time 78.29 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 21 sites = 4 llr = 88 E-value = 4.8e-001
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :::58:::::3::::33::::
pos.-specific C 8:833::8:8:a:8a8:a5a8
probability G 3::::::3:::::3:::::::
matrix T :a33:aa:a38:a:::8:5:3
bits 2.1 * * * *
1.9 * ** * ** * * *
1.7 * ** * ** * * *
1.5 * ** * ** * * *
Information 1.2 *** ************** **
content 1.0 *** *****************
(31.8 bits) 0.8 *** *****************
0.6 *** *****************
0.4 *********************
0.2 *********************
0.0 ---------------------
Multilevel CTCAATTCTCTCTCCCTCCCC
consensus G TCC G TA G AA T T
sequence T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- ---------------------
10657 1511 1.45e-13 CCCAGGCGGT CTCAATTCTCTCTCCCTCCCC TTTCCGTGAC
83796 1801 7.40e-12 TGTATATGCA CTCTCTTCTCTCTCCCTCTCC AGGTCATGCA
6603 1811 1.22e-10 GTAACTTAAT GTTCATTCTCTCTCCCACCCC TAGGTCATGC
20218 606 7.57e-10 CCCAGGCCAG CTCAATTGTTACTGCATCTCT AGGATTGGAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
10657 1.5e-13 1510_[3]_469
83796 7.4e-12 1800_[3]_179
6603 1.2e-10 1810_[3]_169
20218 7.6e-10 605_[3]_1374
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in FASTA format
--------------------------------------------------------------------------------
>10657 pos 1511
CTCAATTCTCTCTCCCTCCCC
>83796 pos 1801
CTCTCTTCTCTCTCCCTCTCC
>6603 pos 1811
GTTCATTCTCTCTCCCACCCC
>20218 pos 606
CTCAATTGTTACTGCATCTCT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 21 n= 7920 bayes= 10.9506 E= 4.8e-001
-865 166 -1 -865
-865 -865 -865 196
-865 166 -865 -4
97 8 -865 -4
156 8 -865 -865
-865 -865 -865 196
-865 -865 -865 196
-865 166 -1 -865
-865 -865 -865 196
-865 166 -865 -4
-3 -865 -865 154
-865 208 -865 -865
-865 -865 -865 196
-865 166 -1 -865
-865 208 -865 -865
-3 166 -865 -865
-3 -865 -865 154
-865 208 -865 -865
-865 108 -865 96
-865 208 -865 -865
-865 166 -865 -4
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 21 n= 7920 E= 4.8e-001
0.000635 0.748719 0.250006 0.000640
0.000635 0.000589 0.000629 0.998147
0.000635 0.748719 0.000629 0.250017
0.499388 0.249966 0.000629 0.250017
0.748765 0.249966 0.000629 0.000640
0.000635 0.000589 0.000629 0.998147
0.000635 0.000589 0.000629 0.998147
0.000635 0.748719 0.250006 0.000640
0.000635 0.000589 0.000629 0.998147
0.000635 0.748719 0.000629 0.250017
0.250012 0.000589 0.000629 0.748770
0.000635 0.998096 0.000629 0.000640
0.000635 0.000589 0.000629 0.998147
0.000635 0.748719 0.250006 0.000640
0.000635 0.998096 0.000629 0.000640
0.250012 0.748719 0.000629 0.000640
0.250012 0.000589 0.000629 0.748770
0.000635 0.998096 0.000629 0.000640
0.000635 0.499343 0.000629 0.499393
0.000635 0.998096 0.000629 0.000640
0.000635 0.748719 0.000629 0.250017
--------------------------------------------------------------------------------
Time 117.82 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
20218 7.77e-19 605_[3(7.57e-10)]_311_[1(6.34e-12)]_582_[2(1.69e-11)]_431
10657 5.46e-22 1_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_7_[1(6.00e-08)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_5_[1(1.18e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_4_[1(1.29e-07)]_332_[2(3.40e-11)]_383_[3(7.75e-07)]_7_[3(1.45e-13)]_56_[3(3.47e-05)]_76_[1(8.70e-12)]_291
83796 1.73e-27 977_[2(4.69e-15)]_281_[1(2.59e-15)]_492_[3(7.40e-12)]_179
6603 9.32e-27 597_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_327_[2(1.62e-15)]_286_[1(2.59e-15)]_475_[3(1.22e-10)]_169
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 3 reached.
********************************************************************************
CPU: hydra-1.lsd.ornl.gov
********************************************************************************
|
