MEME

MEME - Motif discovery tool

MEME version 3.0 (Release date: 2002/04/02 00:11:59)

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= agr3_sub.fasta
ALPHABET= ACDEFGHIKLMNPQRSTVWY
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
A.thaliana               1.0000    865  C.elegans                1.0000    729  
D.melanogaster           1.0000    808  H.sapiens                1.0000    786  
A.aeolicus               1.0000    692  M.thermoautotrophicum    1.0000    677  
B.subtilis               1.0000    689  D.radiodaurans           1.0000    690  
M.tuberculosis           1.0000    673  A.fulgidus               1.0000    642  
A.pernix                 1.0000    681  Hthio                    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 agr3_sub.fasta -protein -nmotifs 10 

model:  mod=         zoops    nmotifs=        10    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           50    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=       12    wnsites=       0.8
theta:  prob=            1    spmap=         pam    spfuzz=        120
em:     prior=       megap    b=           40185    maxiter=        50
        distance=    1e-05
data:   n=            8037    N=              12

sample: seed=            0    seqfrac=         1
Dirichlet mixture priors file: prior30.plib
Letter frequencies in dataset:
A 0.092 C 0.013 D 0.061 E 0.080 F 0.044 G 0.072 H 0.028 I 0.039 K 0.053 
L 0.102 M 0.024 N 0.031 P 0.047 Q 0.032 R 0.059 S 0.062 T 0.045 V 0.059 
W 0.018 Y 0.038 
Background letter frequencies (from dataset with add-one prior applied):
A 0.092 C 0.013 D 0.061 E 0.080 F 0.044 G 0.071 H 0.029 I 0.039 K 0.053 
L 0.102 M 0.024 N 0.031 P 0.047 Q 0.032 R 0.059 S 0.062 T 0.045 V 0.059 
W 0.018 Y 0.038

P N
MOTIF 1 width = 50 sites = 11 llr = 1400 E-value = 7.7e-351

NAME	START	P-VALUE				SITES
			Simplified	A	:	:	:	:	1	8	:	:	:	:	:	:	:	:	:	:	1	:	a	:	3	:	a	1	2	:	1	:	:	:	:	:	:	:	:	:	1	1	:	:	:	:	:	:	:	5	:	:	:	:
			pos.-specific	C	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	a	:	:	a	:	:	:	:	:	:	:	:
			probability	D	:	:	:	:	:	:	2	1	:	:	7	:	:	:	:	:	1	1	:	:	1	:	:	:	1	:	5	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
			matrix	E	:	:	:	:	:	:	:	:	:	:	1	:	:	1	:	:	5	8	:	:	4	3	:	:	1	5	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	5	1	a	:	:
				F	:	:	:	:	:	:	:	:	:	:	:	:	2	:	:	:	:	:	:	9	:	:	:	:	:	:	:	:	:	:	6	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	a
				G	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	8	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	a	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				H	:	:	:	:	9	:	3	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	a	:	:	a	:	:	:	4	:	:	:
				I	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	7	:	:	:	5	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				K	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	7	:	4	3	:	:	7	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	3	:	:	:
				L	:	a	6	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	1	:	1	:	:	:	:	4	8	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				M	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	a	:	:	:	:	:
				N	:	:	:	:	:	:	2	8	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	4	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				P	:	:	:	:	:	:	:	:	a	:	:	:	:	8	:	:	2	:	:	:	:	:	:	:	:	:	:	:	9	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				Q	:	:	:	9	:	1	:	1	:	:	:	:	1	1	:	:	2	1	:	:	1	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:
				R	:	:	4	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	5	2	3	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	2	:	:	:
				S	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	a	:	:	:	8	1	:	:	:	:	:	:	:	:	:	:	a	:
				T	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	7	:	:	:	:	:	:	:	:	:	:	:	:
				V	:	:	:	:	:	:	:	:	:	9	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	3	:	3	:	2	:	5	:	:	1	:	:	:	:	:	:	9	:	:	1	:	:	:
				W	:	:	:	:	:	:	:	:	:	:	:	a	1	:	a	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	a	:	:	:	:	:	:	:	:	:
				Y	a	:	:	:	:	:	3	:	:	:	:	:	5	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	9	:	:	:	:	:	:	:	:	:	:	:	:	:	:
.
			bits	6.3
				5.6
				5.0
				4.4
			Information	3.8
			content	3.1
			(183.6 bits)	2.5
				1.9
				1.3
				0.6
				0.0
.
			Multilevel		`Y`	`L`	`L`	`Q`	`H`	`A`	`H`	`N`	`P`	`V`	`D`	`W`	`Y`	`P`	`W`	`G`	`E`	`E`	`A`	`F`	`E`	`K`	`A`	`R`	`K`	`E`	`D`	`K`	`P`	`I`	`F`	`L`	`S`	`V`	`G`	`Y`	`S`	`T`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`A`	`H`	`E`	`S`	`F`
			consensus				`R`				`Y`														`A`	`E`		`K`		`R`	`N`	`V`		`V`	`L`			`I`												`E`	`K`
			sequence


.

A.aeolicus	15	5.58e-62	`PNRLIKEKSP`		`Y`	`L`	`R`	`Q`	`H`	`A`	`Y`	`N`	`P`	`V`	`D`	`W`	`Y`	`P`	`W`	`G`	`E`	`E`	`A`	`F`	`K`	`K`	`A`	`K`	`E`	`E`	`D`	`K`	`P`	`I`	`F`	`L`	`S`	`I`	`G`	`Y`	`S`	`T`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`E`	`K`	`E`	`S`	`F`	`EDPEIAEILN`
D.melanogaster	86	2.51e-61	`GNRLVASKSP`		`Y`	`L`	`L`	`Q`	`H`	`A`	`Y`	`N`	`P`	`V`	`D`	`W`	`Y`	`P`	`W`	`G`	`E`	`E`	`A`	`F`	`E`	`K`	`A`	`R`	`S`	`E`	`N`	`K`	`I`	`I`	`F`	`L`	`S`	`V`	`G`	`Y`	`S`	`T`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`E`	`H`	`E`	`S`	`F`	`ENPETAAIMN`
A.thaliana	170	1.02e-60	`TNRLAAEHSP`		`Y`	`L`	`L`	`Q`	`H`	`A`	`H`	`N`	`P`	`V`	`D`	`W`	`Y`	`P`	`W`	`G`	`E`	`E`	`A`	`F`	`E`	`E`	`A`	`R`	`K`	`R`	`D`	`V`	`P`	`I`	`F`	`L`	`S`	`I`	`G`	`Y`	`S`	`T`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`E`	`V`	`E`	`S`	`F`	`EDEEVAKLLN`
C.elegans	27	2.48e-60	`KNRLGQEKSP`		`Y`	`L`	`L`	`Q`	`H`	`A`	`N`	`N`	`P`	`I`	`D`	`W`	`Y`	`P`	`W`	`G`	`Q`	`E`	`A`	`F`	`Q`	`K`	`A`	`K`	`D`	`N`	`N`	`K`	`P`	`I`	`F`	`L`	`S`	`V`	`G`	`Y`	`S`	`T`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`E`	`K`	`E`	`S`	`F`	`ENEATAKILN`
H.sapiens	72	3.83e-60	`PNRLIHEKSP`		`Y`	`L`	`L`	`Q`	`H`	`A`	`Y`	`N`	`P`	`V`	`D`	`W`	`Y`	`P`	`W`	`G`	`Q`	`E`	`A`	`F`	`D`	`K`	`A`	`R`	`K`	`E`	`N`	`K`	`P`	`I`	`F`	`L`	`S`	`V`	`G`	`Y`	`S`	`T`	`C`	`H`	`W`	`C`	`H`	`M`	`M`	`E`	`E`	`E`	`S`	`F`	`QNEEIGRLLS`
B.subtilis	17	6.77e-60	`PNRLINEKSP`		`Y`	`L`	`L`	`Q`	`H`	`A`	`H`	`N`	`P`	`V`	`D`	`W`	`F`	`P`	`W`	`G`	`E`	`E`	`A`	`F`	`E`	`K`	`A`	`K`	`R`	`E`	`N`	`K`	`P`	`V`	`L`	`V`	`S`	`I`	`G`	`Y`	`S`	`T`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`A`	`H`	`E`	`S`	`F`	`EDEEIARLLN`
M.thermoautotrophicum	16	4.03e-55	`TNSLIKEKSP`		`Y`	`L`	`L`	`Q`	`H`	`A`	`H`	`N`	`P`	`V`	`N`	`W`	`Y`	`P`	`W`	`G`	`D`	`D`	`A`	`F`	`R`	`K`	`A`	`L`	`A`	`E`	`R`	`K`	`P`	`I`	`F`	`L`	`S`	`I`	`G`	`Y`	`S`	`T`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`A`	`R`	`E`	`S`	`F`	`ENPEIADILN`
D.radiodaurans	26	2.89e-54	`PNRLAQESSP`		`Y`	`L`	`L`	`Q`	`H`	`Q`	`D`	`N`	`P`	`V`	`D`	`W`	`W`	`P`	`W`	`S`	`P`	`E`	`A`	`F`	`A`	`E`	`A`	`R`	`Q`	`R`	`D`	`V`	`P`	`V`	`L`	`L`	`S`	`V`	`G`	`Y`	`S`	`T`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`A`	`H`	`E`	`S`	`F`	`ENERTAAFMN`
A.pernix	13	6.39e-52	`PNRLAEAGSR`		`Y`	`L`	`R`	`Q`	`H`	`S`	`C`	`D`	`P`	`V`	`D`	`W`	`M`	`P`	`W`	`G`	`A`	`E`	`A`	`F`	`E`	`K`	`A`	`R`	`R`	`L`	`D`	`K`	`P`	`V`	`F`	`V`	`S`	`V`	`G`	`Y`	`S`	`S`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`Q`	`R`	`E`	`S`	`F`	`SDPMVAEVLN`
A.fulgidus	12	1.19e-47	`VNRLINSRSP`		`Y`	`L`	`R`	`K`	`A`	`A`	`N`	`Q`	`P`	`V`	`E`	`W`	`F`	`E`	`W`	`G`	`E`	`E`	`A`	`F`	`A`	`K`	`A`	`K`	`K`	`E`	`D`	`K`	`P`	`I`	`L`	`L`	`S`	`I`	`G`	`G`	`V`	`W`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`A`	`K`	`E`	`S`	`F`	`ENEEIAEMIN`
M.tuberculosis	19	3.14e-45	`TNTLALATSP`		`Y`	`L`	`R`	`Q`	`H`	`A`	`D`	`N`	`P`	`V`	`H`	`W`	`Q`	`Q`	`W`	`T`	`P`	`Q`	`A`	`L`	`A`	`E`	`A`	`A`	`A`	`R`	`A`	`V`	`P`	`I`	`L`	`L`	`S`	`V`	`G`	`Y`	`A`	`A`	`C`	`H`	`W`	`C`	`H`	`V`	`M`	`A`	`H`	`E`	`S`	`F`	`DDDEVAAAMN`

Motif 1 block diagrams

Name

Lowest
p-value

Motifs

A.aeolicus

5.6e-62

D.melanogaster

2.5e-61

A.thaliana

1e-60

C.elegans

2.5e-60

H.sapiens

3.8e-60

B.subtilis

6.8e-60

M.thermoautotrophicum

4e-55

D.radiodaurans

2.9e-54

A.pernix

6.4e-52

A.fulgidus

1.2e-47

M.tuberculosis

3.1e-45

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775	800	825	850

Motif 1 in BLOCKS format

BL   MOTIF 1 width=50 seqs=11
A.aeolicus               (   15) YLRQHAYNPVDWYPWGEEAFKKAKEEDKPIFLSIGYSTCHWCHVMEKESF  1 
D.melanogaster           (   86) YLLQHAYNPVDWYPWGEEAFEKARSENKIIFLSVGYSTCHWCHVMEHESF  1 
A.thaliana               (  170) YLLQHAHNPVDWYPWGEEAFEEARKRDVPIFLSIGYSTCHWCHVMEVESF  1 
C.elegans                (   27) YLLQHANNPIDWYPWGQEAFQKAKDNNKPIFLSVGYSTCHWCHVMEKESF  1 
H.sapiens                (   72) YLLQHAYNPVDWYPWGQEAFDKARKENKPIFLSVGYSTCHWCHMMEEESF  1 
B.subtilis               (   17) YLLQHAHNPVDWFPWGEEAFEKAKRENKPVLVSIGYSTCHWCHVMAHESF  1 
M.thermoautotrophicum    (   16) YLLQHAHNPVNWYPWGDDAFRKALAERKPIFLSIGYSTCHWCHVMARESF  1 
D.radiodaurans           (   26) YLLQHQDNPVDWWPWSPEAFAEARQRDVPVLLSVGYSTCHWCHVMAHESF  1 
A.pernix                 (   13) YLRQHSCDPVDWMPWGAEAFEKARRLDKPVFVSVGYSSCHWCHVMQRESF  1 
A.fulgidus               (   12) YLRKAANQPVEWFEWGEEAFAKAKKEDKPILLSIGGVWCHWCHVMAKESF  1 
M.tuberculosis           (   19) YLRQHADNPVHWQQWTPQALAEAAARAVPILLSVGYAACHWCHVMAHESF  1 
//

Motif 1 position-specific scoring matrix

log-odds matrix: alength= 20 w= 50 n= 7449 bayes= 9.29983 E= 7.7e-351 
  -629   -449   -625   -694   -206   -567   -359   -500   -600   -514   -501   -484   -573   -506   -576   -554   -548   -544   -305    466 
  -458   -330   -584   -554   -253   -540   -465   -136   -481    318   -111   -465   -478   -381   -468   -473   -379   -241   -419   -408 
  -440   -354   -560   -493   -281   -507   -396   -178   -222    257   -165   -387   -499   -291    242   -435   -370   -281   -424   -380 
  -295   -256   -368   -160   -422   -423    -47   -306    -77   -296   -165   -181   -317    468   -200   -269   -258   -338   -338   -404 
   -73   -243   -310   -377   -278   -373    481   -377   -367   -371   -282    -78   -372    -62   -233   -240   -258   -360   -312   -123 
   303    -42   -378   -361   -327   -182   -356   -231   -314   -313   -218   -265   -395     28   -342     27   -160   -125   -372   -381 
  -307    226    126   -246   -203   -247    335   -354   -217   -391   -315    229   -335   -118   -262   -158   -203   -362   -327    245 
  -390   -258   -142   -426   -376   -348   -109   -262   -288   -421   -321    476   -370    -94   -351   -151   -211   -348   -355   -358 
  -362   -395   -470   -485   -520   -456   -448   -454   -414   -499   -474   -410    434   -371   -458   -356   -368   -453   -559   -549 
  -198   -152   -439   -430   -318   -450   -384    132   -387   -227   -200   -356   -388   -368   -391   -356   -175    374   -470   -448 
  -352   -310    380    -91   -421   -370    -97   -347   -361   -448   -370     24   -444   -295   -393   -295   -330   -366   -425   -384 
  -450   -294   -445   -471   -164   -438   -391   -364   -401   -295   -304   -346   -455   -339   -391   -407   -379   -363    569   -196 
  -214   -135   -297   -291    192   -328     -8   -160   -239   -213     82   -191   -289     39   -258   -180   -205   -192    130    374 
  -195   -266   -307    -68   -379   -332   -302   -291   -244   -342   -310   -252    404     57   -301   -192   -206   -289   -458   -423 
  -450   -294   -445   -471   -164   -438   -391   -364   -401   -295   -304   -346   -455   -339   -391   -407   -379   -363    569   -196 
  -224   -266   -293   -380   -462    356   -354   -398   -315   -507   -379   -182   -387   -330   -342    -52    -37   -377   -417   -429 
   -17   -509     76    248   -543   -361   -302   -375   -166   -433   -341   -196    155    227   -313   -256   -248   -344   -567   -459 
  -426   -514    -88    351   -609   -482   -433   -456   -373   -576   -488   -321   -503    -51   -490   -430   -415   -480   -606   -574 
   334   -190   -520   -529   -477   -310   -489   -392   -482   -474   -387   -398   -461   -427   -490   -208   -284   -295   -506   -517 
  -369   -183   -459   -472    427   -467   -400   -174   -428   -115   -187   -367   -395   -405   -470   -313   -364   -248   -218    -79 
   116   -310     58    201   -367   -278   -180   -269     80   -324   -226    -94   -261    144     41   -145   -140   -259   -397   -304 
  -323   -403   -198    165   -535   -383   -263   -375    356   -422   -339   -195   -382    -98   -115   -288   -270   -374   -479   -424 
   334   -190   -520   -529   -477   -310   -489   -392   -482   -474   -387   -398   -461   -427   -490   -208   -284   -295   -506   -517 
   -22   -343   -393   -277   -486   -380   -204   -327    271    -39   -284   -185   -389    -69    275   -270   -237   -339   -412   -367 
    62   -224     37     32   -284   -221   -110   -204    197   -259   -159    -30   -214    144    121     53    -74   -201   -316   -226 
  -236   -331   -142    248   -411   -306   -198   -297    -41    -47   -259    134   -305    -53    190   -186   -180   -293   -417   -335 
   -35   -332    292   -191   -457   -236   -206   -418   -208   -484   -407    318   -354   -179     22   -159   -215   -420   -488   -371 
  -359   -324   -456   -364   -457   -427   -298   -203    366   -367   -314   -266   -447   -171   -119   -335   -294    192   -462   -413 
  -206   -272   -335   -333   -384   -343   -316     32   -263   -346   -316   -271    413   -221   -317   -205   -218   -289   -465   -430 
  -346   -239   -476   -490   -297   -498   -484    410   -403   -115   -111   -357   -482   -395   -469   -380   -252    188   -450   -373 
  -467   -308   -637   -629    374   -595   -420   -105   -560    170    -94   -490   -528   -435   -549   -494   -406   -230   -299   -184 
  -382   -257   -558   -502   -190   -528   -427    -36   -431    291    -46   -418   -442   -330   -423   -421   -303    114   -371   -358 
  -342   -304   -513   -597   -539   -422   -503   -512   -497   -581   -497   -337   -472   -466   -509    395   -152   -498   -552   -531 
  -362   -234   -614   -609   -359   -592   -625    347   -548   -221   -214   -487   -565   -538   -612   -502   -289    309   -592   -492 
  -305   -339   -351   -439   -512    371   -406   -458   -372   -560   -441   -245   -441   -389   -396   -297   -381   -448   -462   -479 
  -473   -377   -534   -591   -154     26   -296   -440   -515   -468   -438   -396   -521   -445   -514   -432   -451   -469   -275    450 
     0   -140   -430   -478   -422   -269   -409   -342   -378   -442   -336   -215   -345   -337   -390    358     -5     17   -464   -434 
   -60   -166   -376   -427   -378   -382   -345   -211   -296   -390   -219   -140   -367   -244   -332     71    395   -215    136   -416 
  -412    622   -547   -532   -490   -545   -493   -369   -525   -498   -394   -439   -534   -470   -501   -446   -360   -456   -581   -556 
  -590   -435   -506   -588   -464   -526    508   -578   -561   -567   -502   -304   -525   -290   -447   -473   -477   -577   -486   -333 
  -450   -294   -445   -471   -164   -438   -391   -364   -401   -295   -304   -346   -455   -339   -391   -407   -379   -363    569   -196 
  -412    622   -547   -532   -490   -545   -493   -369   -525   -498   -394   -439   -534   -470   -501   -446   -360   -456   -581   -556 
  -590   -435   -506   -588   -464   -526    508   -578   -561   -567   -502   -304   -525   -290   -447   -473   -477   -577   -486   -333 
  -197   -153   -437   -428   -298   -443   -377     41   -383   -208    105   -352   -384   -359   -386   -348   -175    373   -449   -429 
  -485   -314   -550   -581   -411   -531   -496   -219   -483   -241    528   -444   -505   -452   -556   -455   -404   -320   -368   -367 
   194   -474    -78    248   -559   -361   -315   -384   -174   -443   -352   -205   -331    144   -319   -260   -256   -349   -581   -475 
  -278   -318   -301      9   -430   -340    328   -301    232   -344   -256   -144   -343    -54    160   -217   -196     32   -392   -332 
  -526   -501   -235    360   -611   -528   -478   -478   -538   -632   -548   -368   -619   -334   -570   -517   -496   -538   -603   -600 
  -342   -304   -513   -597   -539   -422   -503   -512   -497   -581   -497   -337   -472   -466   -509    395   -152   -498   -552   -531 
  -413   -228   -494   -515    435   -491   -414   -228   -468   -224   -241   -402   -432   -440   -502   -356   -405   -299   -254   -113

Motif 1 position-specific probability matrix

letter-probability matrix: alength= 20 w= 50 n= 7449 E= 7.7e-351 
 0.001177  0.000575  0.000799  0.000651  0.010620  0.001403  0.002368  0.001223  0.000830  0.002889  0.000747  0.001100  0.000889  0.000951  0.001092  0.001319  0.001017  0.001369  0.002122  0.966858 
 0.003856  0.001311  0.001061  0.001716  0.007685  0.001692  0.001140  0.015312  0.001898  0.925676  0.011130  0.001250  0.001719  0.002266  0.002306  0.002313  0.003280  0.011166  0.000963  0.002260 
 0.004349  0.001108  0.001254  0.002622  0.006340  0.002124  0.001830  0.011432  0.011423  0.606771  0.007651  0.002142  0.001484  0.004238  0.316594  0.003009  0.003484  0.008476  0.000930  0.002739 
 0.011896  0.002182  0.004723  0.026366  0.002378  0.003814  0.020602  0.004690  0.031136  0.013143  0.007685  0.008964  0.005243  0.815512  0.014833  0.009507  0.007587  0.005717  0.001692  0.002328 
 0.055346  0.002391  0.007068  0.005851  0.006466  0.005404  0.802381  0.002874  0.004170  0.007783  0.003419  0.018312  0.003589  0.020728  0.011762  0.011634  0.007568  0.004878  0.002024  0.016351 
 0.750979  0.009645  0.004420  0.006551  0.004610  0.020212  0.002416  0.007936  0.006038  0.011664  0.005313  0.005013  0.003059  0.038642  0.005543  0.074016  0.014910  0.024966  0.001341  0.002726 
 0.010971  0.062020  0.144897  0.014472  0.010846  0.012896  0.290547  0.003382  0.011765  0.006766  0.002709  0.153592  0.004614  0.014032  0.009633  0.020650  0.011098  0.004842  0.001833  0.208435 
 0.006180  0.002151  0.022624  0.004173  0.003288  0.006426  0.013394  0.006401  0.007235  0.005516  0.002598  0.852453  0.003635  0.016564  0.005191  0.021627  0.010526  0.005310  0.001505  0.003203 
 0.007507  0.000833  0.002329  0.002772  0.001213  0.003031  0.001278  0.001681  0.003014  0.003215  0.000898  0.001827  0.952984  0.002427  0.002472  0.005202  0.003528  0.002572  0.000367  0.000849 
 0.023316  0.004492  0.002896  0.004049  0.004911  0.003151  0.001987  0.097958  0.003636  0.021224  0.006012  0.002666  0.003211  0.002485  0.003927  0.005234  0.013475  0.792977  0.000680  0.001713 
 0.008016  0.001504  0.843282  0.042477  0.002396  0.005486  0.014550  0.003552  0.004340  0.004577  0.001852  0.036957  0.002168  0.004105  0.003886  0.007974  0.004604  0.004685  0.000928  0.002661 
 0.004066  0.001685  0.002785  0.003040  0.014246  0.003433  0.001897  0.003142  0.003287  0.013223  0.002922  0.002854  0.002010  0.003025  0.003932  0.003667  0.003277  0.004807  0.912886  0.009816 
 0.020824  0.005054  0.007770  0.010654  0.168123  0.007345  0.026984  0.012898  0.010129  0.023228  0.042552  0.008356  0.006369  0.041748  0.009911  0.017688  0.010929  0.015642  0.043477  0.510319 
 0.023899  0.002048  0.007203  0.049888  0.003212  0.007168  0.003527  0.005212  0.009810  0.009538  0.002814  0.005488  0.777858  0.047029  0.007356  0.016272  0.010891  0.008009  0.000735  0.002042 
 0.004066  0.001685  0.002785  0.003040  0.014246  0.003433  0.001897  0.003142  0.003287  0.013223  0.002922  0.002854  0.002010  0.003025  0.003932  0.003667  0.003277  0.004807  0.912886  0.009816 
 0.019431  0.002043  0.007978  0.005715  0.001801  0.841433  0.002463  0.002487  0.005976  0.003035  0.001741  0.008892  0.003217  0.003218  0.005540  0.042801  0.034954  0.004343  0.000980  0.001951 
 0.081981  0.000380  0.103024  0.445538  0.001032  0.005850  0.003522  0.002911  0.016756  0.005084  0.002269  0.008057  0.138037  0.152794  0.006786  0.010441  0.008122  0.005478  0.000345  0.001593 
 0.004819  0.000365  0.033089  0.910891  0.000654  0.002526  0.001419  0.001659  0.003991  0.001885  0.000816  0.003391  0.001441  0.022287  0.001987  0.003129  0.002546  0.002124  0.000264  0.000715 
 0.934277  0.003453  0.001652  0.002034  0.001627  0.008312  0.000966  0.002595  0.001884  0.003818  0.001642  0.001989  0.001934  0.001647  0.001984  0.014593  0.006327  0.007678  0.000527  0.001062 
 0.007156  0.003634  0.002520  0.003030  0.854939  0.002809  0.001789  0.011703  0.002727  0.046028  0.006608  0.002463  0.003043  0.001912  0.002284  0.007040  0.003622  0.010607  0.003899  0.022185 
 0.205412  0.001504  0.091012  0.321456  0.003482  0.010379  0.008210  0.006065  0.092524  0.010772  0.005011  0.016336  0.007704  0.086282  0.078567  0.022518  0.017124  0.009874  0.001126  0.004640 
 0.009808  0.000789  0.015428  0.250339  0.001091  0.005010  0.004623  0.002918  0.625425  0.005465  0.002300  0.008101  0.003351  0.016158  0.026720  0.008375  0.006981  0.004452  0.000638  0.002027 
 0.934277  0.003453  0.001652  0.002034  0.001627  0.008312  0.000966  0.002595  0.001884  0.003818  0.001642  0.001989  0.001934  0.001647  0.001984  0.014593  0.006327  0.007678  0.000527  0.001062 
 0.079065  0.001199  0.003986  0.011708  0.001527  0.005134  0.006938  0.004063  0.347091  0.077780  0.003356  0.008739  0.003187  0.019694  0.398655  0.009448  0.008738  0.005678  0.001016  0.002996 
 0.141844  0.002730  0.078480  0.099845  0.006186  0.015451  0.013314  0.009525  0.207899  0.016982  0.008012  0.025587  0.010712  0.085913  0.136564  0.089193  0.027085  0.014729  0.001973  0.007977 
 0.017883  0.001300  0.022676  0.446666  0.002577  0.008583  0.007212  0.005002  0.040013  0.073884  0.003994  0.079459  0.005697  0.022076  0.220422  0.016994  0.013052  0.007790  0.000981  0.003739 
 0.072427  0.001295  0.459270  0.021189  0.001873  0.013956  0.006836  0.002159  0.012525  0.003569  0.001430  0.283770  0.004066  0.009170  0.069084  0.020390  0.010228  0.003237  0.000598  0.002928 
 0.007640  0.001366  0.002567  0.006406  0.001869  0.003718  0.003621  0.009597  0.669801  0.007996  0.002735  0.004957  0.002129  0.009705  0.026002  0.006021  0.005906  0.225064  0.000718  0.002182 
 0.022018  0.001958  0.005959  0.007940  0.003104  0.006626  0.003190  0.049040  0.008609  0.009292  0.002696  0.004814  0.825757  0.006850  0.006591  0.014885  0.010002  0.008019  0.000702  0.001946 
 0.008386  0.002457  0.002239  0.002667  0.005663  0.002258  0.000998  0.672589  0.003248  0.046110  0.011120  0.002639  0.001673  0.002056  0.002288  0.004418  0.007894  0.217635  0.000781  0.002878 
 0.003614  0.001531  0.000733  0.001021  0.592082  0.001157  0.001558  0.019006  0.001094  0.330870  0.012520  0.001049  0.001211  0.001562  0.001314  0.002008  0.002709  0.012061  0.002212  0.010687 
 0.006511  0.002169  0.001269  0.002459  0.011931  0.001842  0.001479  0.030533  0.002684  0.767097  0.017563  0.001728  0.002200  0.003229  0.003150  0.003323  0.005540  0.130764  0.001342  0.003188 
 0.008605  0.001564  0.001727  0.001270  0.001060  0.003846  0.000873  0.001124  0.001695  0.001818  0.000768  0.003028  0.001794  0.001254  0.001737  0.948784  0.015830  0.001876  0.000384  0.000961 
 0.007507  
motif=2
starts: w=8, seq=0, l=865          
starts: w=8, seq=5, l=677          
starts: w=8, seq=10, l=681          
starts: w=11, seq=0, l=865          
starts: w=11, seq=5, l=677          
starts: w=11, seq=10, l=681          
starts: w=15, seq=0, l=865          
starts: w=15, seq=5, l=677          
starts: w=15, seq=10, l=681          
starts: w=21, seq=0, l=865          
starts: w=21, seq=5, l=677          
starts: w=21, seq=10, l=681          
starts: w=29, seq=0, l=865          
starts: w=29, seq=5, l=677          
starts: w=29, seq=10, l=681          
starts: w=41, seq=0, l=865          
starts: w=41, seq=5, l=677          
starts: w=41, seq=10, l=681          
starts: w=50, seq=0, l=865          
starts: w=50, seq=5, l=677          
starts: w=50, seq=10, l=681          

em: w=   8, psites=   2, iter=   0 
em: w=   8, psites=   4, iter=   0 
em: w=   8, psites=   8, iter=   0 
em: w=   8, psites=  12, iter=   0 
em: w=  11, psites=   2, iter=   0 
em: w=  11, psites=   4, iter=   0 
em: w=  11, psites=   8, iter=   0 
em: w=  11, psites=  12, iter=   0 
em: w=  15, psites=   2, iter=   0 
em: w=  15, psites=   4, iter=   0 
em: w=  15, psites=   8, iter=   0 
em: w=  15, psites=  12, iter=   0 
em: w=  21, psites=   2, iter=   0 
em: w=  21, psites=   4, iter=   0 
em: w=  21, psites=   8, iter=   0 
em: w=  21, psites=  12, iter=   0 
em: w=  29, psites=   2, iter=   0 
em: w=  29, psites=   4, iter=   0 
em: w=  29, psites=   8, iter=   0 
em: w=  29, psites=  12, iter=   0 
em: w=  41, psites=   2, iter=   0 
em: w=  41, psites=   4, iter=   0 
em: w=  41, psites=   8, iter=   0 
em: w=  41, psites=  12, iter=   0 
em: w=  50, psites=   2, iter=   0 
em: w=  50, psites=   4, iter=   0 
em: w=  50, psites=   8, iter=   0 
em: w=  50, psites=  12, iter=   0 0.002557  0.000859  0.001170  0.003700  0.001179  0.000374  0.435214  0.001188  0.022028  0.005468  0.001073  0.000940  0.000765  0.000850  0.001895  0.006102  0.505575  0.000291  0.001264 
 0.011150  0.001229  0.005337  0.003796  0.001274  0.936810  0.001712  0.001643  0.004026  0.002105  0.001130  0.005748  0.002224  0.002138  0.003795  0.007883  0.003238  0.002662  0.000716  0.001385 
 0.003462  0.000949  0.001494  0.001327  0.015298  0.085666  0.003669  0.001858  0.001498  0.003988  0.001159  0.002013  0.001270  0.001450  0.001678  0.003091  0.001992  0.002302  0.002617  0.863218 
 0.092129  0.004892  0.003083  0.002906  0.002387  0.011063  0.001680  0.003662  0.003873  0.004770  0.002339  0.007099  0.004315  0.003081  0.003967  0.735620  0.043875  0.066663  0.000709  0.001888 
 0.060657  0.004088  0.004491  0.004144  0.003240  0.005076  0.002620  0.009097  0.006816  0.006857  0.005264  0.011920  0.003717  0.005839  0.005918  0.100514  0.698915  0.013391  0.045299  0.002136 
 0.005301  0.962160  0.001365  0.001992  0.001492  0.001638  0.000936  0.003034  0.001396  0.003225  0.001571  0.001497  0.001165  0.001223  0.001836  0.002802  0.003736  0.002507  0.000314  0.000809 
 0.001543  0.000634  0.001822  0.001359  0.001788  0.001871  0.964981  0.000713  0.001090  0.002008  0.000740  0.003807  0.001236  0.004256  0.002681  0.002326  0.001656  0.001089  0.000607  0.003792 
 0.004066  0.001685  0.002785  0.003040  0.014246  0.003433  0.001897  0.003142  0.003287  0.013223  0.002922  0.002854  0.002010  0.003025  0.003932  0.003667  0.003277  0.004807  0.912886  0.009816 
 0.005301  0.962160  0.001365  0.001992  0.001492  0.001638  0.000936  0.003034  0.001396  0.003225  0.001571  0.001497  0.001165  0.001223  0.001836  0.002802  0.003736  0.002507  0.000314  0.000809 
 0.001543  0.000634  0.001822  0.001359  0.001788  0.001871  0.964981  0.000713  0.001090  0.002008  0.000740  0.003807  0.001236  0.004256  0.002681  0.002326  0.001656  0.001089  0.000607  0.003792 
 0.023561  0.004461  0.002928  0.004119  0.005613  0.003325  0.002087  0.052049  0.003742  0.024128  0.049941  0.002732  0.003299  0.002634  0.004076  0.005533  0.013481  0.789562  0.000784  0.001947 
 0.003186  0.001465  0.001339  0.001422  0.002571  0.001805  0.000918  0.008590  0.001862  0.019247  0.935892  0.001443  0.001421  0.001389  0.001257  0.002623  0.002760  0.006436  0.001371  0.003003 
 0.352609  0.000483  0.035245  0.446178  0.000924  0.005864  0.003211  0.002734  0.015911  0.004726  0.002092  0.007570  0.004770  0.086331  0.006484  0.010153  0.007695  0.005282  0.000314  0.001422 
 0.013424  0.001424  0.007532  0.084854  0.002259  0.006785  0.278245  0.004860  0.265178  0.009411  0.004077  0.011547  0.004388  0.021891  0.179494  0.013686  0.011651  0.074295  0.001166  0.003834 
 0.002410  0.000400  0.011890  0.964409  0.000643  0.001843  0.001040  0.001432  0.001277  0.001274  0.000540  0.002458  0.000645  0.003146  0.001143  0.001708  0.001452  0.001420  0.000270  0.000599 
 0.008605  0.001564  0.001727  0.001270  0.001060  0.003846  0.000873  0.001124  0.001695  0.001818  0.000768  0.003028  0.001794  0.001254  0.001737  0.948784  0.015830  0.001876  0.000384  0.000961 
 0.005258  0.002657  0.001971  0.002253  0.903964  0.002384  0.001617  0.008082  0.002074  0.021639  0.004525  0.001935  0.002366  0.001507  0.001823  0.005204  0.002728  0.007489  0.003031  0.017490






Time 27.00 secs.

P N
MOTIF 2 width = 50 sites = 11 llr = 1281 E-value = 1.4e-285

NAME	START	P-VALUE				SITES
			Simplified	A	:	:	3	:	:	:	:	:	:	:	:	:	:	:	:	4	:	:	:	2	2	:	1	6	1	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	1	1	:	:	:	5	1	:	:	:
			pos.-specific	C	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	4	:	:	:	:	:	:	1	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:
			probability	D	:	:	:	:	:	:	a	:	1	:	:	:	a	:	a	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	6	:	:	:	:	:	:	:	:	:	:
			matrix	E	:	:	:	:	:	:	:	:	9	a	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	3	:	:	:	:	:	:	:	:
				F	a	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	5	:	:	:	:	:	:	:	:	:	:	:	:	:	:	5	:	:	:	:	:	:	:	7	4	:	:	:	:	7
				G	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	9	2	9	a	:	:	:	:	:	:	:	:	:	:	4	:	:	:	:	4	9	:	:	:
				H	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:
				I	:	:	:	7	:	:	:	:	:	:	:	:	:	4	:	:	2	:	:	:	1	:	:	1	:	:	:	:	:	:	:	:	:	:	2	2	1	:	:	:	:	:	:	1	:	:	:	:	:	1
				K	:	:	:	:	a	:	:	:	:	:	:	:	:	:	:	5	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	4	:	:	:	:	:	:	:	:
				L	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	2	1	:	:	:	1	1	1	3	:	:	:	:	:	:	:	5	:	:	1	7	:	:	:	4	:	:	2	:	:	:	:	:	1
				M	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	9	:	:	:	1	2	3	:	:	:	:	:	:	:	5	:	:	:	2	:	:	:	:	:	:	:	1	:	:	:	:	:
				N	:	:	2	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	3	:	:	:	:	:	2	:	:	:	:	:	:	:	:	:	:
				P	:	:	1	:	:	:	:	:	:	:	:	a	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	a	:	:	:	:	:	:	a	:	:	:	a	:	:	:	:	:	:	:
				Q	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	1	:	:	5	:	:	:	:	3	:	:	:	:	:	:	:	:	:	:	:	:	1	1	:	:	:	:	:	:	:	:
				R	:	:	:	:	:	:	:	a	:	:	a	:	:	:	:	:	1	:	:	3	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:
				S	:	:	3	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	2	:	:	:	:	2	3	1	3	:	:	:	:	:	3	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:
				T	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	1	:	2	:	:	2	5	:	1	:	:	:	:	:	5	:	:	:	9	:	1	:	:	:	:	1	:	:	a	:	:
				V	:	a	:	3	:	a	:	:	:	:	:	:	:	6	:	:	5	:	:	:	2	4	2	:	:	:	:	:	:	:	:	:	:	:	7	:	:	:	:	:	:	:	:	:	2	1	:	:	:	:
				W	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	a	:	:	:	:	2	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				Y	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	9	:	:	1	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	3	:	:	:	a	1
.
			bits	6.3
				5.6
				5.0
				4.4
			Information	3.8
			content	3.1
			(168.0 bits)	2.5
				1.9
				1.3
				0.6
				0.0
.
			Multilevel		`F`	`V`	`A`	`I`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`V`	`D`	`K`	`V`	`Y`	`M`	`R`	`F`	`C`	`Q`	`A`	`L`	`T`	`G`	`Q`	`G`	`G`	`W`	`P`	`L`	`T`	`V`	`F`	`L`	`T`	`P`	`D`	`G`	`K`	`P`	`F`	`F`	`A`	`G`	`T`	`Y`	`F`
			consensus				`S`	`V`										`I`		`A`						`V`			`M`	`S`		`S`					`M`	`N`							`L`	`E`			`Y`	`G`
			sequence																																			`S`


.

B.subtilis	79	6.10e-56	`EEIARLLNER`		`F`	`V`	`A`	`I`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`V`	`D`	`S`	`V`	`Y`	`M`	`R`	`I`	`C`	`Q`	`L`	`M`	`T`	`G`	`Q`	`G`	`G`	`W`	`P`	`L`	`N`	`V`	`F`	`I`	`T`	`P`	`D`	`Q`	`K`	`P`	`F`	`Y`	`A`	`G`	`T`	`Y`	`F`	`PKTSKFNRPG`
D.radiodaurans	88	9.51e-56	`ERTAAFMNAH`		`F`	`V`	`N`	`I`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`V`	`D`	`A`	`V`	`Y`	`M`	`A`	`A`	`T`	`Q`	`A`	`L`	`T`	`G`	`Q`	`G`	`G`	`W`	`P`	`M`	`T`	`V`	`F`	`L`	`T`	`P`	`D`	`A`	`E`	`P`	`F`	`Y`	`A`	`G`	`T`	`Y`	`F`	`PPQEGMGMPS`
M.thermoautotrophicum	78	3.77e-52	`PEIADILNRD`		`F`	`V`	`S`	`V`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`I`	`D`	`A`	`I`	`Y`	`M`	`R`	`V`	`C`	`Q`	`M`	`M`	`T`	`G`	`A`	`G`	`G`	`W`	`P`	`L`	`T`	`I`	`I`	`M`	`T`	`P`	`E`	`G`	`E`	`P`	`F`	`F`	`A`	`G`	`T`	`Y`	`F`	`PPEDRGGVPG`
A.aeolicus	77	1.56e-51	`PEIAEILNNY`		`F`	`V`	`P`	`I`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`V`	`D`	`A`	`F`	`Y`	`M`	`S`	`V`	`C`	`Q`	`A`	`M`	`T`	`G`	`T`	`G`	`G`	`W`	`P`	`L`	`T`	`I`	`I`	`M`	`T`	`P`	`D`	`K`	`E`	`P`	`F`	`F`	`A`	`G`	`T`	`Y`	`I`	`PKEGMFGRPG`
M.tuberculosis	81	3.92e-51	`DEVAAAMNAG`		`F`	`V`	`C`	`I`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`I`	`D`	`A`	`V`	`Y`	`M`	`N`	`A`	`T`	`V`	`A`	`L`	`T`	`G`	`Q`	`G`	`G`	`W`	`P`	`M`	`T`	`C`	`F`	`L`	`T`	`P`	`N`	`G`	`R`	`P`	`F`	`F`	`C`	`G`	`T`	`Y`	`Y`	`PKAAFLQLLS`
H.sapiens	134	3.92e-51	`EEIGRLLSED`		`F`	`V`	`S`	`V`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`V`	`D`	`K`	`V`	`Y`	`M`	`T`	`F`	`V`	`Q`	`A`	`T`	`S`	`S`	`G`	`G`	`G`	`W`	`P`	`M`	`N`	`V`	`W`	`L`	`T`	`P`	`N`	`L`	`Q`	`P`	`F`	`V`	`G`	`G`	`T`	`Y`	`F`	`PPEDGLTRVG`
A.thaliana	232	4.39e-51	`EEVAKLLNNS`		`F`	`V`	`S`	`I`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`V`	`D`	`K`	`V`	`Y`	`M`	`S`	`F`	`V`	`Q`	`A`	`L`	`Y`	`G`	`G`	`G`	`G`	`W`	`P`	`L`	`S`	`V`	`F`	`L`	`S`	`P`	`D`	`L`	`K`	`P`	`L`	`M`	`G`	`G`	`T`	`Y`	`F`	`PPNDNYGRPG`
C.elegans	89	1.09e-50	`EATAKILNDN`		`F`	`V`	`A`	`I`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`V`	`D`	`K`	`L`	`Y`	`M`	`A`	`F`	`V`	`V`	`A`	`S`	`S`	`G`	`H`	`G`	`G`	`W`	`P`	`M`	`S`	`V`	`F`	`L`	`T`	`P`	`D`	`L`	`H`	`P`	`I`	`T`	`G`	`G`	`T`	`Y`	`F`	`PPDDNRGMLG`
A.fulgidus	74	1.10e-49	`EEIAEMINRN`		`F`	`V`	`A`	`I`	`K`	`V`	`D`	`R`	`D`	`E`	`R`	`P`	`D`	`I`	`D`	`K`	`R`	`Y`	`Q`	`E`	`F`	`V`	`M`	`A`	`T`	`T`	`G`	`S`	`G`	`G`	`W`	`P`	`L`	`T`	`V`	`F`	`L`	`T`	`P`	`D`	`G`	`K`	`P`	`F`	`F`	`G`	`G`	`T`	`Y`	`F`	`PPEDRYHLPG`
D.melanogaster	148	1.61e-47	`PETAAIMNEN`		`F`	`V`	`N`	`I`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`I`	`D`	`K`	`I`	`Y`	`M`	`Q`	`F`	`L`	`L`	`M`	`S`	`K`	`G`	`S`	`G`	`G`	`W`	`P`	`M`	`S`	`V`	`W`	`L`	`T`	`P`	`T`	`L`	`A`	`P`	`L`	`V`	`A`	`G`	`T`	`Y`	`F`	`PPKSRYGMPS`
A.pernix	75	1.51e-43	`PMVAEVLNRA`		`F`	`V`	`M`	`V`	`K`	`V`	`D`	`R`	`E`	`E`	`R`	`P`	`D`	`V`	`D`	`T`	`L`	`L`	`M`	`R`	`Y`	`C`	`A`	`I`	`A`	`S`	`G`	`S`	`C`	`G`	`W`	`P`	`L`	`N`	`V`	`L`	`L`	`T`	`P`	`D`	`G`	`K`	`P`	`F`	`Y`	`V`	`A`	`T`	`Y`	`L`	`PKESLVALAV`

Motif 2 block diagrams

Name

Lowest
p-value

Motifs

B.subtilis

6.1e-56

D.radiodaurans

9.5e-56

M.thermoautotrophicum

3.8e-52

A.aeolicus

1.6e-51

M.tuberculosis

3.9e-51

H.sapiens

3.9e-51

A.thaliana

4.4e-51

C.elegans

1.1e-50

A.fulgidus

1.1e-49

D.melanogaster

1.6e-47

A.pernix

1.5e-43

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775	800	825	850

Motif 2 in BLOCKS format

BL   MOTIF 2 width=50 seqs=11
B.subtilis               (   79) FVAIKVDREERPDVDSVYMRICQLMTGQGGWPLNVFITPDQKPFYAGTYF  1 
D.radiodaurans           (   88) FVNIKVDREERPDVDAVYMAATQALTGQGGWPMTVFLTPDAEPFYAGTYF  1 
M.thermoautotrophicum    (   78) FVSVKVDREERPDIDAIYMRVCQMMTGAGGWPLTIIMTPEGEPFFAGTYF  1 
A.aeolicus               (   77) FVPIKVDREERPDVDAFYMSVCQAMTGTGGWPLTIIMTPDKEPFFAGTYI  1 
M.tuberculosis           (   81) FVCIKVDREERPDIDAVYMNATVALTGQGGWPMTCFLTPNGRPFFCGTYY  1 
H.sapiens                (  134) FVSVKVDREERPDVDKVYMTFVQATSSGGGWPMNVWLTPNLQPFVGGTYF  1 
A.thaliana               (  232) FVSIKVDREERPDVDKVYMSFVQALYGGGGWPLSVFLSPDLKPLMGGTYF  1 
C.elegans                (   89) FVAIKVDREERPDVDKLYMAFVVASSGHGGWPMSVFLTPDLHPITGGTYF  1 
A.fulgidus               (   74) FVAIKVDRDERPDIDKRYQEFVMATTGSGGWPLTVFLTPDGKPFFGGTYF  1 
D.melanogaster           (  148) FVNIKVDREERPDIDKIYMQFLLMSKGSGGWPMSVWLTPTLAPLVAGTYF  1 
A.pernix                 (   75) FVMVKVDREERPDVDTLLMRYCAIASGSCGWPLNVLLTPDGKPFYVATYL  1 
//

Motif 2 position-specific scoring matrix

log-odds matrix: alength= 20 w= 50 n= 7449 bayes= 10.9361 E= 1.4e-285 
  -413   -228   -494   -515    435   -491   -414   -228   -468   -224   -241   -402   -432   -440   -502   -356   -405   -299   -254   -113 
  -293   -240   -517   -524   -398   -491   -465    -48   -476   -312   -290   -436   -461   -451   -479   -425   -270    394   -528   -503 
   154    237   -257   -225   -303   -235   -230   -186   -159   -279    150    211     55   -130   -230    189   -107   -177   -360   -301 
  -346   -239   -476   -490   -297   -498   -484    410   -403   -115   -111   -357   -482   -395   -469   -380   -252    188   -450   -373 
  -402   -320   -498   -474   -548   -475   -398   -358    411   -500   -397   -306   -447   -345    -80   -421   -355   -458   -455   -494 
  -293   -240   -517   -524   -398   -491   -465    -48   -476   -312   -290   -436   -461   -451   -479   -425   -270    394   -528   -503 
  -369   -324    387   -149   -436   -385   -293   -363   -379   -463   -387    -42   -457   -313   -409   -313   -347   -383   -438   -400 
  -488   -338   -540   -570   -556   -486   -339   -466   -231   -522   -481   -375   -452   -309    401   -449   -439   -551   -442   -513 
  -508   -502   -181    358   -610   -521   -470   -473   -506   -624   -538   -358   -601   -315   -557   -502   -483   -529   -603   -596 
  -526   -501   -235    360   -611   -528   -478   -478   -538   -632   -548   -368   -619   -334   -570   -517   -496   -538   -603   -600 
  -488   -338   -540   -570   -556   -486   -339   -466   -231   -522   -481   -375   -452   -309    401   -449   -439   -551   -442   -513 
  -362   -395   -470   -485   -520   -456   -448   -454   -414   -499   -474   -410    434   -371   -458   -356   -368   -453   -559   -549 
  -369   -324    387   -149   -436   -385   -293   -363   -379   -463   -387    -42   -457   -313   -409   -313   -347   -383   -438   -400 
  -338   -224   -600   -591   -359   -580   -591    312   -538   -232   -222   -482   -543   -525   -585   -492   -277    333   -591   -499 
  -369   -324    387   -149   -436   -385   -293   -363   -379   -463   -387    -42   -457   -313   -409   -313   -347   -383   -438   -400 
   178   -191   -267   -236   -396   -253   -238   -302    283   -367   -272   -143   -313   -127   -179     61     92   -271   -419   -354 
  -191   -120   -422   -388     50   -365   -300    215   -316     52    -73   -271   -346   -266     -6   -252   -136    289   -302   -261 
  -483   -332   -545   -560    -49   -530   -210   -295   -472    -19   -295   -365   -507   -381   -461   -423   -418   -360   -169    444 
  -474   -305   -541   -565   -401   -525   -486   -210   -462   -231    526   -433   -499   -176   -536   -444   -393   -311   -360   -357 
    62   -219   -125     30   -279   -216   -106   -200    -14   -255   -155    134   -210    143    167    121     83   -197   -312   -222 
    52   -115   -425   -384    318   -349   -255    123   -307   -127    -71   -254   -342   -252   -327   -228   -144    137   -235    103 
  -252    447   -507   -466   -242   -407   -381     19   -388     -1   -126   -332   -417   -336   -413   -295    176    251   -368   -314 
   -51   -148   -371   -234   -212   -353   -134    -55   -243    -35    127   -200   -317    405   -253   -222   -155    101   -285   -261 
   261   -131   -475   -439   -205   -318   -376    116   -374      3    245   -331   -430   -318   -394   -199   -206    -86   -342   -321 
    -1    -97   -369   -324   -168   -294   -251    -13   -246    118    307   -204   -309   -197   -279    123    177    -46   -263   -214 
  -259   -170   -331   -370   -363   -379   -309   -208     -6   -375   -213   -117   -353   -212   -290    178    368   -217   -396     20 
  -237   -281   -291   -378   -462    362   -352   -398   -312   -509   -380   -182   -391   -331   -339    -64   -317   -385   -413   -427 
    -1   -215   -139   -114   -304     88    128   -223    -48   -282   -183    -33   -234    266   -132    177     87   -218   -339   -249 
  -244    140   -304   -391   -471    362   -364   -408   -324   -517   -390   -196   -400   -343   -350   -239   -324   -393   -423   -437 
  -305   -339   -351   -439   -512    371   -406   -458   -372   -560   -441   -245   -441   -389   -396   -297   -381   -448   -462   -479 
  -450   -294   -445   -471   -164   -438   -391   -364   -401   -295   -304   -346   -455   -339   -391   -407   -379   -363    569   -196 
  -362   -395   -470   -485   -520   -456   -448   -454   -414   -499   -474   -410    434   -371   -458   -356   -368   -453   -559   -549 
  -473   -331   -727   -673   -176   -645   -531    -69   -597    239    403   -568   -560   -435   -568   -579   -398   -202   -382   -389 
  -256   -190   -249   -357   -400   -317   -297   -251   -275   -417   -257    246   -361   -232   -331    181    348   -253   -432   -407 
  -184    175   -424   -414   -311   -435   -366    176   -371   -225   -195   -341   -372   -351   -374   -339   -162    358   -454   -436 
  -408   -255   -565   -556    366   -531   -375    181   -490      9   -103   -422   -475   -399   -496   -407   -352   -210    278   -133 
  -392   -265   -554   -493   -171   -528   -414     97   -422    284    230   -414   -432   -314   -410   -419   -309   -160   -353   -347 
  -256   -170   -374   -430   -382   -388   -347   -215   -299   -396   -223   -140   -370   -247   -335     70    413   -219   -412   -421 
  -362   -395   -470   -485   -520   -456   -448   -454   -414   -499   -474   -410    434   -371   -458   -356   -368   -453   -559   -549 
  -351   -312    376    -83   -424   -360   -273   -350   -351   -450   -373     76   -439   -286   -390   -285   -134   -369   -428   -385 
   -10   -211   -203   -155   -289    189   -164   -166     95    136   -164    -89   -274    138   -105   -137   -122   -183   -333   -262 
   -12   -264   -179    143   -339   -267    131   -244    247   -295   -199    -75   -261    146     70   -129   -121   -243   -350   -270 
  -362   -395   -470   -485   -520   -456   -448   -454   -414   -499   -474   -410    434   -371   -458   -356   -368   -453   -559   -549 
  -386   -206   -493   -502    412   -495   -425     20   -456     -2   -141   -397   -422   -413   -490   -346   -368   -226   -245   -115 
  -205   -120   -334   -317    253   -329    -66    -71   -257   -160    124   -208   -303   -218   -275   -191     39     99   -138    307 
   240    249   -476   -473   -415    199   -437   -314   -428   -407   -311   -321   -376   -354   -431   -119   -186     42   -460   -463 
  -103   -278   -292   -379   -462    362   -353   -397   -312   -508   -379   -183   -391   -332   -338   -229   -315   -383   -413   -427 
  -399   -320   -515   -584   -520   -475   -485   -383   -465   -539   -402   -317   -489   -413   -490   -201    438   -386   -534   -541 
  -629   -449   -625   -694   -206   -567   -359   -500   -600   -514   -501   -484   -573   -506   -576   -554   -548   -544   -305    466 
  -365   -180   -455   -468    423   -464   -398    -71   -425   -123   -189   -364   -392   -403   -467   -309   -362   -248   -215    -12

Motif 2 position-specific probability matrix

letter-probability matrix: alength= 20 w= 50 n= 7449 E= 1.4e-285 
 0.005258  0.002657  0.001971  0.002253  0.903964  0.002384  0.001617  0.008082  0.002074  0.021639  0.004525  0.001935  0.002366  0.001507  0.001823  0.005204  0.002728  0.007489  0.003031  0.017490 
 0.012119  0.002439  0.001681  0.002115  0.002821  0.002374  0.001136  0.028176  0.001959  0.011700  0.003230  0.001532  0.001928  0.001395  0.002141  0.003245  0.006953  0.911430  0.000454  0.001171 
 0.266880  0.066781  0.010187  0.016743  0.005447  0.014046  0.005793  0.010768  0.017634  0.014783  0.068219  0.135602  0.068908  0.012860  0.012044  0.228171  0.021573  0.017356  0.001448  0.004755 
 0.008386  0.002457  0.002239  0.002667  0.005663  0.002258  0.000998  0.672589  0.003248  0.046110  0.011120  0.002639  0.001673  0.002056  0.002288  0.004418  0.007894  0.217635  0.000781  0.002878 
 0.005687  0.001405  0.001921  0.002977  0.000998  0.002660  0.001815  0.003270  0.920150  0.003196  0.001539  0.003766  0.002124  0.002915  0.033907  0.003337  0.003856  0.002481  0.000753  0.001245 
 0.012119  0.002439  0.001681  0.002115  0.002821  0.002374  0.001136  0.028176  0.001959  0.011700  0.003230  0.001532  0.001928  0.001395  0.002141  0.003245  0.006953  0.911430  0.000454  0.001171 
 0.007132  0.001363  0.888432  0.028371  0.002159  0.004951  0.003743  0.003163  0.003841  0.004111  0.001647  0.023440  0.001990  0.003637  0.003479  0.007044  0.004092  0.004175  0.000844  0.002388 
 0.003126  0.001238  0.001442  0.001536  0.000942  0.002463  0.002724  0.001553  0.010720  0.002732  0.000855  0.002341  0.002057  0.003743  0.954420  0.002737  0.002157  0.001299  0.000824  0.001090 
 0.002714  0.000398  0.017271  0.956856  0.000649  0.001934  0.001098  0.001481  0.001597  0.001354  0.000579  0.002620  0.000732  0.003575  0.001247  0.001895  0.001596  0.001520  0.000270  0.000616 
 0.002410  0.000400  0.011890  0.964409  0.000643  0.001843  0.001040  0.001432  0.001277  0.001274  0.000540  0.002458  0.000645  0.003146  0.001143  0.001708  0.001452  0.001420  0.000270  0.000599 
 0.003126  0.001238  0.001442  0.001536  0.000942  0.002463  0.002724  0.001553  0.010720  0.002732  0.000855  0.002341  0.002057  0.003743  0.954420  0.002737  0.002157  0.001299  0.000824  0.001090 
 0.007507  0.000833  0.002329  0.002772  0.001213  0.003031  0.001278  0.001681  0.003014  0.003215  0.000898  0.001827  0.952984  0.002427  0.002472  0.005202  0.003528  0.002572  0.000367  0.000849 
 0.007132  0.001363  0.888432  0.028371  0.002159  0.004951  0.003743  0.003163  0.003841  0.004111  0.001647  0.023440  0.001990  0.003637  0.003479  0.007044  0.004092  0.004175  0.000844  0.002388 
 0.008826  0.002732  0.000951  0.001328  0.003680  0.001284  0.000476  0.341999  0.001274  0.020461  0.005164  0.001115  0.001092  0.000834  0.001028  0.002029  0.006632  0.597599  0.000294  0.001203 
 0.007132  0.001363  0.888432  0.028371  0.002159  0.004951  0.003743  0.003163  0.003841  0.004111  0.001647  0.023440  0.001990  0.003637  0.003479  0.007044  0.004092  0.004175  0.000844  0.002388 
 0.316382  0.003446  0.009562  0.015501  0.002857  0.012373  0.005471  0.004823  0.377308  0.008003  0.003666  0.011617  0.005395  0.013194  0.017152  0.094090  0.085837  0.009075  0.000967  0.003281 
 0.024427  0.005627  0.003249  0.005428  0.063020  0.005694  0.003566  0.173728  0.005945  0.146744  0.014540  0.004787  0.004293  0.005019  0.056811  0.010736  0.017665  0.440264  0.002175  0.006282 
 0.003236  0.001293  0.001388  0.001646  0.031603  0.001819  0.006678  0.005072  0.002013  0.089157  0.003122  0.002501  0.001409  0.002261  0.002429  0.003281  0.002508  0.004880  0.005458  0.828248 
 0.003451  0.001553  0.001427  0.001586  0.002764  0.001876  0.000983  0.009160  0.002157  0.020589  0.923279  0.001561  0.001482  0.009356  0.001446  0.002831  0.002964  0.006854  0.001456  0.003225 
 0.141660  0.002825  0.025518  0.097954  0.006402  0.015966  0.013652  0.009788  0.048086  0.017398  0.008217  0.079245  0.010976  0.085687  0.187906  0.142681  0.080687  0.015111  0.002025  0.008216 
 0.131628  0.005817  0.003194  0.005558  0.402118  0.006347  0.004877  0.091825  0.006329  0.042165  0.014689  0.005398  0.004421  0.005521  0.006146  0.012703  0.016734  0.153178  0.003454  0.077897 
 0.016079  0.286806  0.001805  0.003148  0.008277  0.004248  0.002039  0.044591  0.003602  0.101532  0.010027  0.003139  0.002627  0.003095  0.003388  0.007956  0.153840  0.338095  0.001371  0.004334 
 0.064501  0.004634  0.004628  0.015755  0.010240  0.006201  0.011300  0.026723  0.009852  0.080102  0.058164  0.007847  0.005232  0.527881  0.010262  0.013210  0.015455  0.119321  0.002442  0.006251 
 0.562912  0.005220  0.002262  0.003798  0.010693  0.007895  0.002101  0.087554  0.003990  0.104307  0.131434  0.003169  0.002393  0.003495  0.003856  0.015480  0.010897  0.032764  0.001647  0.004133 
 0.091670  0.006592  0.004687  0.008448  0.013872  0.009311  0.005004  0.035818  0.009688  0.230399  0.202207  0.007640  0.005531  0.008107  0.008544  0.143989  0.154009  0.042990  0.002846  0.008647 
 0.015343  0.003981  0.006135  0.006128  0.003595  0.005179  0.003343  0.009305  0.051032  0.007602  0.005494  0.013942  0.004076  0.007290  0.007905  0.210753  0.580679  0.013227  0.001135  0.043856 
 0.017875  0.001841  0.008088  0.005800  0.001802  0.876307  0.002487  0.002479  0.006114  0.002993  0.001731  0.008899  0.003129  0.003194  0.005665  0.039460  0.005037  0.004114  0.001005  0.001983 
 0.091280  0.002916  0.023091  0.036310  0.005408  0.131263  0.069219  0.008352  0.038074  0.014440  0.006756  0.025046  0.009306  0.200426  0.023777  0.209897  0.082852  0.013114  0.001684  0.006788 
 0.016925  0.034115  0.007368  0.005304  0.001696  0.877490  0.002296  0.002322  0.005605  0.002828  0.001612  0.008095  0.002957  0.002953  0.005227  0.011736  0.004787  0.003894  0.000940  0.001850 
 0.011150  0.001229  0.005337  0.003796  0.001274  0.936810  0.001712  0.001643  0.004026  0.002105  0.001130  0.005748  0.002224  0.002138  0.003795  0.007883  0.003238  0.002662  0.000716  0.001385 
 0.004066  0.001685  0.002785  0.003040  0.014246  0.003433  0.001897  0.003142  0.003287  0.013223  0.002922  0.002854  0.002010  0.003025  0.003932  0.003667  0.003277  0.004807  0.912886  0.009816 
 0.007507  0.000833  0.002329  0.002772  0.001213  0.003031  0.001278  0.001681  0.003014  0.003215  0.000898  0.001827  0.952984  0.002427  0.002472  0.005202  0.003528  0.002572  0.000367  0.000849 
 0.003470  0.001301  0.000392  0.000753  0.013081  0.000818  0.000721  0.024292  0.000850  0.535104  0.392499  0.000611  0.000974  0.001558  0.001151  0.001110  0.002873  0.014611  0.001249  0.002585 
 0.015625  0.003452  0.010799  0.006705  0.002784  0.007938  0.003642  0.006884  0.007913  0.005654  0.004060  0.172680  0.003859  0.006374  0.005967  0.215495  0.506764  0.010249  0.000881  0.002275 
 0.025743  0.043488  0.003221  0.004519  0.005158  0.003503  0.002255  0.133106  0.004061  0.021403  0.006221  0.002961  0.003575  0.002790  0.004429  0.005865  0.014704  0.710382  0.000760  0.001857 
 0.005441  0.002204  0.001205  0.001695  0.560810  0.001799  0.002115  0.137271  0.001781  0.108751  0.011774  0.001689  0.001751  0.001995  0.001896  0.003654  0.003942  0.013822  0.121243  0.015163 
 0.006104  0.002054  0.001305  0.002612  0.013621  0.001843  0.001624  0.076720  0.002854  0.728561  0.118278  0.001784  0.002360  0.003594  0.003455  0.003376  0.005316  0.019572  0.001527  0.003440 
 0.015575  0.003977  0.004531  0.004054  
motif=3
starts: w=8, seq=0, l=865          
starts: w=8, seq=5, l=677          
starts: w=8, seq=10, l=681          
starts: w=11, seq=0, l=865          
starts: w=11, seq=5, l=677          
starts: w=11, seq=10, l=681          
starts: w=15, seq=0, l=865          
starts: w=15, seq=5, l=677          
starts: w=15, seq=10, l=681          
starts: w=21, seq=0, l=865          
starts: w=21, seq=5, l=677          
starts: w=21, seq=10, l=681          
starts: w=29, seq=0, l=865          
starts: w=29, seq=5, l=677          
starts: w=29, seq=10, l=681          
starts: w=41, seq=0, l=865          
starts: w=41, seq=5, l=677          
starts: w=41, seq=10, l=681          
starts: w=50, seq=0, l=865          
starts: w=50, seq=5, l=677          
starts: w=50, seq=10, l=681          

em: w=   8, psites=   2, iter=   0 
em: w=   8, psites=   2, iter=  10 
em: w=   8, psites=   4, iter=   0 
em: w=   8, psites=   8, iter=   0 
em: w=   8, psites=  12, iter=   0 
em: w=  11, psites=   2, iter=   0 
em: w=  11, psites=   4, iter=   0 
em: w=  11, psites=   8, iter=   0 
em: w=  11, psites=  12, iter=   0 
em: w=  15, psites=   2, iter=   0 
em: w=  15, psites=   4, iter=   0 
em: w=  15, psites=   8, iter=   0 
em: w=  15, psites=  12, iter=   0 
em: w=  21, psites=   2, iter=   0 
em: w=  21, psites=   4, iter=   0 
em: w=  21, psites=   8, iter=   0 
em: w=  21, psites=  12, iter=   0 
em: w=  29, psites=   2, iter=   0 
em: w=  29, psites=   4, iter=   0 
em: w=  29, psites=   8, iter=   0 
em: w=  29, psites=  12, iter=   0 
em: w=  41, psites=   2, iter=   0 
em: w=  41, psites=   4, iter=   0 
em: w=  41, psites=   8, iter=   0 
em: w=  41, psites=  12, iter=   0 
em: w=  50, psites=   2, iter=   0 
em: w=  50, psites=   4, iter=   0 
em: w=  50, psites=   8, iter=   0 
em: w=  50, psites=  12, iter=   0 0.003136  0.004868  0.002583  0.008860  0.006702  0.006562  0.005136  0.011939  0.003632  0.005733  0.005817  0.100257  0.790524  0.013031  0.001011  0.002070 
 0.007507  0.000833  0.002329  0.002772  0.001213  0.003031  0.001278  0.001681  0.003014  0.003215  0.000898  0.001827  0.952984  0.002427  0.002472  0.005202  0.003528  0.002572  0.000367  0.000849 
 0.008108  0.001484  0.820205  0.045000  0.002356  0.005884  0.004317  0.003466  0.004674  0.004501  0.001819  0.053033  0.002257  0.004364  0.003979  0.008536  0.017858  0.004594  0.000906  0.002658 
 0.086210  0.003000  0.014877  0.027253  0.005989  0.265392  0.009147  0.012410  0.102760  0.262148  0.007706  0.016963  0.007053  0.082560  0.028663  0.023775  0.019393  0.016727  0.001755  0.006221 
 0.084887  0.002069  0.017549  0.215349  0.004252  0.011256  0.070587  0.007212  0.294257  0.013212  0.006069  0.018695  0.007701  0.087450  0.096241  0.025184  0.019589  0.010979  0.001560  0.005902 
 0.007507  0.000833  0.002329  0.002772  0.001213  0.003031  0.001278  0.001681  0.003014  0.003215  0.000898  0.001827  0.952984  0.002427  0.002472  0.005202  0.003528  0.002572  0.000367  0.000849 
 0.006349  0.003091  0.001990  0.002465  0.775102  0.002317  0.001503  0.045112  0.002255  0.100510  0.009062  0.002007  0.002526  0.001811  0.001985  0.005588  0.003529  0.012381  0.003226  0.017192 
 0.022272  0.005611  0.006000  0.008868  0.256795  0.007323  0.018093  0.023963  0.008976  0.033686  0.056871  0.007450  0.005771  0.007005  0.008782  0.016334  0.059432  0.117861  0.006768  0.322137 
 0.485390  0.072661  0.002243  0.003013  0.002505  0.283047  0.001385  0.004456  0.002733  0.006085  0.002790  0.003397  0.003483  0.002732  0.002979  0.026990  0.012518  0.079328  0.000727  0.001539 
 0.044947  0.001875  0.008016  0.005781  0.001808  0.876042  0.002475  0.002497  0.006103  0.003013  0.001743  0.008815  0.003147  0.003190  0.005671  0.012619  0.005100  0.004170  0.001008  0.001982 
 0.005803  0.001403  0.001708  0.001397  0.001205  0.002652  0.000988  0.002759  0.002118  0.002440  0.001489  0.003498  0.001586  0.001817  0.001986  0.015315  0.946413  0.004089  0.000436  0.000899 
 0.001177  0.000575  0.000799  0.000651  0.010620  0.001403  0.002368  0.001223  0.000830  0.002889  0.000747  0.001100  0.000889  0.000951  0.001092  0.001319  0.001017  0.001369  0.002122  0.966858 
 0.007317  0.003720  0.002585  0.003110  0.831008  0.002871  0.001812  0.024054  0.002795  0.043627  0.006502  0.002522  0.003113  0.001938  0.002330  0.007234  0.003689  0.010656  0.003971  0.035145






Time 51.89 secs.

P N
MOTIF 3 width = 50 sites = 11 llr = 1195 E-value = 2.0e-246

NAME	START	P-VALUE				SITES
			Simplified	A	2	3	1	:	:	:	:	2	:	5	1	:	:	:	:	:	:	:	:	:	:	:	3	:	:	2	:	:	2	1	:	:	:	:	:	:	:	:	:	:	:	:	:	7	:	1	2	1	5	:
			pos.-specific	C	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
			probability	D	:	:	:	:	:	:	3	:	:	:	1	:	:	:	:	a	:	:	:	:	:	:	:	:	:	:	:	6	1	2	:	:	:	:	:	:	:	:	:	:	:	a	:	:	:	:	:	:	:	:
			matrix	E	:	:	2	1	:	:	2	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	1	1	3	:	:	:	:	:	:	a	:	:	:	:	:	:	:	1	:	:	:	:	:
				F	:	:	:	1	:	:	:	:	:	:	1	:	:	:	:	:	:	:	1	1	:	9	1	:	:	:	:	:	:	:	:	:	:	:	:	8	:	:	:	:	:	:	:	:	:	:	:	1	:	1
				G	:	:	:	1	:	1	:	1	:	2	:	9	a	:	:	:	:	:	7	5	a	:	:	:	:	:	:	1	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	2	:	:	:	:	:	:
				H	:	:	:	2	:	:	:	1	:	:	:	:	:	:	4	:	6	:	:	:	:	:	6	:	:	:	:	:	:	:	:	4	:	:	a	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				I	:	1	1	1	:	:	:	:	1	:	:	:	:	8	:	:	:	4	:	:	:	:	:	:	:	:	:	:	:	:	:	1	2	:	:	:	:	:	:	:	:	:	:	:	:	1	1	:	:	:
				K	:	:	:	3	:	:	1	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	a	:	:	:	:	:	:	:	:	:	:	:	:
				L	:	2	3	1	:	9	:	:	:	1	:	:	:	:	:	:	1	4	1	:	:	1	:	:	:	:	:	:	:	:	:	2	2	:	:	:	:	:	:	a	:	:	:	:	3	8	5	:	1	2
				M	7	:	:	:	:	:	:	2	9	:	1	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	a	:	:	:	:	:	1	:	2	1	:	:
				N	1	:	:	:	:	:	1	1	:	:	3	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	4	:	:	:	:	1	:	:
				P	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	9	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				Q	:	:	1	:	:	:	1	1	:	:	:	:	:	:	:	:	3	:	:	1	:	:	:	:	:	:	:	:	1	2	:	:	:	:	:	:	:	:	:	:	:	:	6	:	5	:	:	1	:	:
				R	:	:	1	1	:	:	1	1	:	2	2	:	:	:	1	:	:	:	:	:	:	:	:	a	:	:	:	:	3	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	2	:	:
				S	:	:	:	:	1	:	:	2	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	8	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:
				T	:	:	2	:	9	:	2	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	5	2	:	1	:	1	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	2	2	:
				V	:	5	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	3	:	:	:	:	:	:	:	:	5	:	:	:	:	2	5	1	:	:	:	:	:	:	:	:	:	:	:	:	1	1	2	:
				W	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	a	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:
				Y	:	:	:	:	:	:	:	:	:	:	1	:	:	:	5	:	:	:	:	2	:	:	:	:	a	:	:	:	:	:	:	:	:	:	:	2	:	:	:	:	a	:	:	:	:	:	:	1	:	7
.
			bits	6.3
				5.6
				5.0
				4.4
			Information	3.8
			content	3.1
			(156.8 bits)	2.5
				1.9
				1.3
				0.6
				0.0
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			Multilevel		`M`	`V`	`L`	`K`	`T`	`L`	`D`	`x`	`M`	`A`	`N`	`G`	`G`	`I`	`Y`	`D`	`H`	`I`	`G`	`G`	`G`	`F`	`H`	`R`	`Y`	`S`	`V`	`D`	`R`	`E`	`W`	`H`	`V`	`P`	`H`	`F`	`E`	`K`	`M`	`L`	`Y`	`D`	`Q`	`A`	`Q`	`L`	`L`	`x`	`A`	`Y`
			consensus			`A`													`H`		`Q`	`L`					`A`				`T`																`N`		`L`
			sequence																			`V`


.

H.sapiens	296	2.65e-54	`LTQDGSRAQQ`		`M`	`A`	`L`	`H`	`T`	`L`	`K`	`M`	`M`	`A`	`N`	`G`	`G`	`I`	`R`	`D`	`H`	`V`	`G`	`Q`	`G`	`F`	`H`	`R`	`Y`	`S`	`T`	`D`	`R`	`Q`	`W`	`H`	`V`	`P`	`H`	`F`	`E`	`K`	`M`	`L`	`Y`	`D`	`Q`	`A`	`Q`	`L`	`A`	`V`	`A`	`Y`	`SQAFQLSGDE`
A.thaliana	391	5.80e-51	`KTSEADEEKS`		`M`	`V`	`L`	`F`	`S`	`L`	`Q`	`G`	`M`	`A`	`N`	`G`	`G`	`M`	`H`	`D`	`H`	`I`	`G`	`G`	`G`	`F`	`H`	`R`	`Y`	`S`	`V`	`D`	`E`	`C`	`W`	`H`	`V`	`P`	`H`	`F`	`E`	`K`	`M`	`L`	`Y`	`D`	`Q`	`G`	`Q`	`L`	`A`	`N`	`V`	`Y`	`LDGFSITKDV`
B.subtilis	233	6.59e-51	`HNTGQENALY`		`N`	`V`	`T`	`K`	`T`	`L`	`D`	`S`	`M`	`A`	`N`	`G`	`G`	`I`	`Y`	`D`	`H`	`I`	`G`	`Y`	`G`	`F`	`A`	`R`	`Y`	`S`	`T`	`D`	`D`	`E`	`W`	`L`	`V`	`P`	`H`	`F`	`E`	`K`	`M`	`L`	`Y`	`D`	`N`	`A`	`L`	`L`	`L`	`T`	`A`	`Y`	`TEAYQVTQNS`
A.aeolicus	231	1.24e-50	`YRYKREQALK`		`M`	`I`	`E`	`K`	`T`	`L`	`T`	`N`	`M`	`R`	`M`	`G`	`G`	`I`	`Y`	`D`	`H`	`V`	`G`	`F`	`G`	`F`	`H`	`R`	`Y`	`S`	`T`	`D`	`R`	`E`	`W`	`I`	`L`	`P`	`H`	`F`	`E`	`K`	`M`	`L`	`Y`	`D`	`Q`	`A`	`M`	`L`	`L`	`F`	`A`	`Y`	`TEGYQLLKKD`
C.elegans	247	7.81e-50	`ESEKAKDSIM`		`M`	`L`	`Q`	`K`	`T`	`L`	`E`	`S`	`M`	`A`	`D`	`G`	`G`	`I`	`H`	`D`	`H`	`I`	`G`	`N`	`G`	`F`	`H`	`R`	`Y`	`S`	`V`	`G`	`S`	`E`	`W`	`H`	`I`	`P`	`H`	`F`	`E`	`K`	`M`	`L`	`Y`	`D`	`Q`	`S`	`Q`	`L`	`L`	`A`	`T`	`Y`	`SDFHKLTERK`
D.radiodaurans	237	2.89e-49	`FLLTQPQGRE`		`M`	`A`	`L`	`H`	`T`	`L`	`R`	`M`	`M`	`G`	`A`	`G`	`G`	`I`	`Y`	`D`	`Q`	`L`	`G`	`G`	`G`	`F`	`H`	`R`	`Y`	`S`	`V`	`D`	`A`	`Q`	`W`	`L`	`V`	`P`	`H`	`F`	`E`	`K`	`M`	`L`	`Y`	`D`	`N`	`A`	`Q`	`L`	`V`	`R`	`T`	`L`	`LRAYQLTGED`
M.tuberculosis	231	1.45e-45	`ERTRSPAALE`		`A`	`V`	`A`	`R`	`T`	`G`	`N`	`A`	`M`	`A`	`R`	`G`	`G`	`I`	`Y`	`D`	`Q`	`L`	`G`	`G`	`G`	`F`	`A`	`R`	`Y`	`S`	`V`	`D`	`G`	`A`	`W`	`V`	`V`	`P`	`H`	`F`	`E`	`K`	`M`	`L`	`Y`	`D`	`N`	`A`	`L`	`L`	`L`	`R`	`A`	`Y`	`AHWARRTGDP`
M.thermoautotrophicum	229	1.47e-44	`LRRGEGEALE`		`M`	`V`	`R`	`L`	`T`	`L`	`E`	`R`	`M`	`R`	`Y`	`G`	`G`	`I`	`Y`	`D`	`Q`	`L`	`G`	`Y`	`G`	`F`	`H`	`R`	`Y`	`A`	`V`	`E`	`P`	`T`	`W`	`T`	`I`	`P`	`H`	`F`	`E`	`K`	`M`	`L`	`Y`	`D`	`Q`	`A`	`L`	`A`	`M`	`T`	`A`	`Y`	`LEAFQVTGDE`
A.fulgidus	228	2.97e-43	`FFTGDEEVLK`		`A`	`A`	`E`	`I`	`T`	`L`	`D`	`A`	`M`	`A`	`R`	`G`	`G`	`I`	`Y`	`D`	`H`	`L`	`L`	`G`	`G`	`F`	`F`	`R`	`Y`	`S`	`T`	`D`	`A`	`K`	`W`	`V`	`T`	`P`	`H`	`Y`	`E`	`K`	`M`	`L`	`Y`	`D`	`N`	`A`	`E`	`L`	`L`	`Y`	`L`	`Y`	`SIAYALTGKR`
D.melanogaster	308	3.59e-43	`LVTKDPDVLD`		`M`	`V`	`I`	`E`	`T`	`L`	`T`	`Q`	`I`	`G`	`K`	`G`	`G`	`I`	`H`	`D`	`H`	`I`	`F`	`G`	`G`	`F`	`A`	`R`	`Y`	`A`	`T`	`T`	`Q`	`D`	`W`	`H`	`N`	`V`	`H`	`F`	`E`	`K`	`M`	`L`	`Y`	`D`	`Q`	`G`	`Q`	`L`	`M`	`M`	`A`	`F`	`ANAYKVTRDE`
A.pernix	224	4.84e-37	`SMAGDRRALN`		`M`	`L`	`T`	`G`	`T`	`L`	`D`	`H`	`M`	`L`	`F`	`S`	`G`	`V`	`H`	`D`	`L`	`V`	`E`	`G`	`G`	`L`	`H`	`R`	`Y`	`S`	`V`	`T`	`R`	`D`	`W`	`R`	`L`	`P`	`H`	`Y`	`E`	`K`	`M`	`L`	`Y`	`D`	`Q`	`A`	`W`	`I`	`I`	`Q`	`V`	`L`	`AEAYAASGDR`

Motif 3 block diagrams

Name

Lowest
p-value

Motifs

H.sapiens

2.7e-54

A.thaliana

5.8e-51

B.subtilis

6.6e-51

A.aeolicus

1.2e-50

C.elegans

7.8e-50

D.radiodaurans

2.9e-49

M.tuberculosis

1.5e-45

M.thermoautotrophicum

1.5e-44

A.fulgidus

3e-43

D.melanogaster

3.6e-43

A.pernix

4.8e-37

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775	800	825	850

Motif 3 in BLOCKS format

BL   MOTIF 3 width=50 seqs=11
H.sapiens                (  296) MALHTLKMMANGGIRDHVGQGFHRYSTDRQWHVPHFEKMLYDQAQLAVAY  1 
A.thaliana               (  391) MVLFSLQGMANGGMHDHIGGGFHRYSVDECWHVPHFEKMLYDQGQLANVY  1 
B.subtilis               (  233) NVTKTLDSMANGGIYDHIGYGFARYSTDDEWLVPHFEKMLYDNALLLTAY  1 
A.aeolicus               (  231) MIEKTLTNMRMGGIYDHVGFGFHRYSTDREWILPHFEKMLYDQAMLLFAY  1 
C.elegans                (  247) MLQKTLESMADGGIHDHIGNGFHRYSVGSEWHIPHFEKMLYDQSQLLATY  1 
D.radiodaurans           (  237) MALHTLRMMGAGGIYDQLGGGFHRYSVDAQWLVPHFEKMLYDNAQLVRTL  1 
M.tuberculosis           (  231) AVARTGNAMARGGIYDQLGGGFARYSVDGAWVVPHFEKMLYDNALLLRAY  1 
M.thermoautotrophicum    (  229) MVRLTLERMRYGGIYDQLGYGFHRYAVEPTWTIPHFEKMLYDQALAMTAY  1 
A.fulgidus               (  228) AAEITLDAMARGGIYDHLLGGFFRYSTDAKWVTPHYEKMLYDNAELLYLY  1 
D.melanogaster           (  308) MVIETLTQIGKGGIHDHIFGGFARYATTQDWHNVHFEKMLYDQGQLMMAF  1 
A.pernix                 (  224) MLTGTLDHMLFSGVHDLVEGGLHRYSVTRDWRLPHYEKMLYDQAWIIQVL  1 
//

Motif 3 position-specific scoring matrix

log-odds matrix: alength= 20 w= 50 n= 7449 bayes= 10.4288 E= 2.0e-246 
    46   -199   -411   -435   -378   -314   -399   -225   -356   -291    490     87   -399   -328   -405   -215   -236   -254   -409   -379 
   119   -175   -510   -482   -273   -461   -415    154   -417     63   -153   -369   -437   -376   -438   -355   -207    294   -419   -368 
    -5   -178   -153     87   -238   -232   -126     86    -40     88   -119    -50   -226    137     43    -91    158   -138   -293   -214 
  -138   -208   -137     26     44     -6    207     72    196    -50   -145    -34   -216      0     49    -79    -73   -180   -306   -211 
  -256   -170   -374   -430   -382   -388   -347   -215   -299   -396   -223   -140   -370   -247   -335     70    413   -219   -412   -421 
  -376   -273   -524   -483   -225    -41   -409   -103   -410    305    -72   -393   -421   -318   -402   -383   -313   -198   -384   -368 
  -146   -234    165     99   -295   -225   -119   -214     90   -269   -169    135   -221    143     47    -85    157   -211   -327   -236 
    62   -216   -125    -82   -276     -6    121   -196    -14   -252    223    133   -209    143     48    121    -68   -193   -310   -219 
  -475   -304   -546   -574   -390   -530   -491   -114   -476   -222    526   -438   -501   -443   -550   -449   -392   -295   -359   -358 
   268    -70   -359   -331   -328     59   -319   -222   -228    -84   -217   -236   -370   -230     74    -84   -160   -145   -375   -364 
    -5   -213     35    -83     42   -217   -104   -190     91   -248    133    254   -209      5    118    -72    -69   -190   -305     72 
  -237   -281   -291   -378   -462    362   -352   -398   -312   -509   -380   -182   -391   -331   -339    -64   -317   -385   -413   -427 
  -305   -339   -351   -439   -512    371   -406   -458   -372   -560   -441   -245   -441   -389   -396   -297   -381   -448   -462   -479 
  -332   -241   -426   -443   -263   -457   -429    416   -351    -70     52   -308   -442   -342   -416   -332   -230    119   -396   -326 
  -426   -300   -460   -467    -23   -478    344   -320   -312   -347   -309   -283   -458   -285     40   -357   -363   -358   -150    373 
  -369   -324    387   -149   -436   -385   -293   -363   -379   -463   -387    -42   -457   -313   -409   -313   -347   -383   -438   -400 
  -358   -219   -264   -323   -224   -368    459   -324   -290   -146   -225    -25   -335    177   -171   -215   -224   -321   -260    -66 
  -367   -242   -589   -580   -284   -563   -547    327   -506    161   -144   -452   -536   -464   -553   -463   -288    215   -480   -425 
  -239   -281   -284   -135    -71    352   -340   -362   -300   -182   -353   -175   -388   -317   -329   -230   -312   -363   -399   -395 
  -283   -292   -250   -321     55    304   -236   -324   -258   -394   -319    105   -385     87   -314   -228   -271   -340   -262    168 
  -305   -339   -351   -439   -512    371   -406   -458   -372   -560   -441   -245   -441   -389   -396   -297   -381   -448   -462   -479 
  -369   -183   -459   -472    427   -467   -400   -174   -428   -115   -187   -367   -395   -405   -470   -313   -364   -248   -218    -79 
   103   -235   -353   -407     74   -366    441   -309   -367   -340   -274   -134   -391   -125   -283   -244   -260   -317   -235    -60 
  -488   -338   -540   -570   -556   -486   -339   -466   -231   -522   -481   -375   -452   -309    401   -449   -439   -551   -442   -513 
  -629   -449   -625   -694   -206   -567   -359   -500   -600   -514   -501   -484   -573   -506   -576   -554   -548   -544   -305    466 
    92   -150   -460   -508   -464   -262   -443   -403   -431   -487   -378   -260   -360   -365   -434    359    -73   -327   -500   -481 
  -280   -215   -564   -568   -371   -429   -528    -19   -493   -269   -245   -399   -485   -451   -527   -295    314    308   -535   -467 
  -340   -320    368    -50   -433   -131   -264   -359   -314   -455   -377    -20   -418   -250   -376   -261     12   -374   -440   -387 
    62   -220     37     32   -279     -6   -107   -200    -16   -255   -155    -24     43    143    166     54    -70   -197   -312   -222 
    -6    212    113    140   -286   -222   -113   -206     90   -261   -161    -30   -214    213   -106    -79     82   -202   -319   -228 
  -450   -294   -445   -471   -164   -438   -391   -364   -401   -295   -304   -346   -455   -339   -391   -407   -379   -363    569   -196 
  -170    -86   -372   -323   -144   -304    313    138   -236     72    -37   -198   -304   -186     23   -183     88    152   -240   -188 
  -180   -116   -410   -382   -213   -368   -304    210   -315     31    -99     67   -342   -273   -329   -257     49    302   -323   -281 
  -204   -269   -334   -332   -386   -340   -316   -290   -262   -350   -319   -270    413   -221   -316   -202   -216    -20   -466   -431 
  -590   -435   -506   -588   -464   -526    508   -578   -561   -567   -502   -304   -525   -290   -447   -473   -477   -577   -486   -333 
  -421   -232   -499   -515    417   -498   -288   -233   -455   -231   -243   -365   -439   -397   -472   -356   -395   -300   -181    160 
  -526   -501   -235    360   -611   -528   -478   -478   -538   -632   -548   -368   -619   -334   -570   -517   -496   -538   -603   -600 
  -402   -320   -498   -474   -548   -475   -398   -358    411   -500   -397   -306   -447   -345    -80   -421   -355   -458   -455   -494 
  -485   -314   -550   -581   -411   -531   -496   -219   -483   -241    528   -444   -505   -452   -556   -455   -404   -320   -368   -367 
  -458   -330   -584   -554   -253   -540   -465   -136   -481    318   -111   -465   -478   -381   -468   -473   -379   -241   -419   -408 
  -629   -449   -625   -694   -206   -567   -359   -500   -600   -514   -501   -484   -573   -506   -576   -554   -548   -544   -305    466 
  -369   -324    387   -149   -436   -385   -293   -363   -379   -463   -387    -42   -457   -313   -409   -313   -347   -383   -438   -400 
  -365   -367   -189   -282   -488   -298   -250   -478   -221   -515   -437    338   -405    416   -297   -227   -278   -476   -506   -405 
   294    -70   -419   -410   -367     71   -393   -275   -365   -357   -260   -290   -387   -319   -383     44   -173   -166   -410   -420 
  -244   -208   -315    -55   -293   -365    -73   -166   -187     13     70   -162   -301    425   -204   -220   -190   -204     80   -310 
  -110   -233   -503   -443   -172   -481   -373     73   -371    294    -17   -364   -390   -275   -363   -366   -270   -131   -341   -327 
    52   -169   -490   -437   -173   -414   -342    128   -359    219    249   -318   -388   -285   -368   -299   -195     69   -313   -279 
    -6   -154   -173   -128     57   -240   -132    -87    -60   -183    146    124   -234    131    115   -100    158     47   -274     86 
   260    -70   -409   -380   -260   -232   -339    -78   -320    -55   -149   -273   -383   -281   -346   -112    129    115   -343   -318 
  -392   -271   -464   -466    138   -474   -142   -260   -398     59   -254   -311   -440   -328   -398   -342   -351   -315   -138    410

Motif 3 position-specific probability matrix

letter-probability matrix: alength= 20 w= 50 n= 7449 E= 2.0e-246 
 0.126578  0.003245  0.003523  0.003927  0.003232  0.008132  0.001796  0.008227  0.004518  0.013534  0.719407  0.057354  0.002967  0.003277  0.003579  0.013882  0.008822  0.010194  0.001036  0.002771 
 0.210305  0.003845  0.001772  0.002822  0.006696  0.002924  0.001605  0.113970  0.002941  0.158250  0.008332  0.002429  0.002277  0.002343  0.002838  0.005239  0.010759  0.456713  0.000963  0.002977 
 0.088788  0.003753  0.020946  0.146297  0.008559  0.014297  0.011896  0.070979  0.040347  0.187818  0.010541  0.022190  0.009874  0.082015  0.079839  0.032802  0.135279  0.022825  0.002312  0.008645 
 0.035493  0.003051  0.023552  0.095589  0.060273  0.068463  0.119791  0.064793  0.206869  0.072334  0.008784  0.024883  0.010569  0.031677  0.083033  0.035501  0.027353  0.017026  0.002110  0.008857 
 0.015575  0.003977  0.004531  0.004054  0.003136  0.004868  0.002583  0.008860  0.006702  0.006562  0.005136  0.011939  0.003632  0.005733  0.005817  0.100257  0.790524  0.013031  0.001011  0.002070 
 0.006805  0.001941  0.001610  0.002798  0.009334  0.053967  0.001678  0.019267  0.003096  0.844352  0.014631  0.002054  0.002544  0.003506  0.003637  0.004336  0.005173  0.015055  0.001227  0.002989 
 0.033465  0.002545  0.191060  0.158958  0.005747  0.015012  0.012550  0.008868  0.099088  0.015791  0.007438  0.079833  0.010193  0.085634  0.082009  0.034202  0.134561  0.013779  0.001825  0.007442 
 0.142004  0.002893  0.025433  0.045296  0.006561  0.068350  0.066170  0.010110  0.048196  0.017820  0.112980  0.078853  0.011083  0.085567  0.082321  0.142170  0.028233  0.015544  0.002061  0.008354 
 0.003414  0.001573  0.001377  0.001498  0.002968  0.001809  0.000953  0.017809  0.001960  0.021931  0.920920  0.001511  0.001464  0.001473  0.001307  0.002739  0.002984  0.007656  0.001461  0.003195 
 0.591137  0.007959  0.005025  0.008030  0.004560  0.107793  0.003126  0.008439  0.010949  0.057154  0.005343  0.006121  0.003635  0.006450  0.098880  0.034274  0.014970  0.021778  0.001306  0.003069 
 0.088848  0.002950  0.077262  0.044898  0.059523  0.015928  0.013850  0.010495  0.099924  0.018243  0.060663  0.182934  0.011046  0.032992  0.134087  0.037250  0.028151  0.015939  0.002132  0.062887 
 0.017875  0.001841  0.008088  0.005800  0.001802  0.876307  0.002487  0.002479  0.006114  0.002993  0.001731  0.008899  0.003129  0.003194  0.005665  0.039460  0.005037  0.004114  0.001005  0.001983 
 0.011150  0.001229  0.005337  0.003796  0.001274  0.936810  0.001712  0.001643  0.004026  0.002105  0.001130  0.005748  0.002224  0.002138  0.003795  0.007883  0.003238  0.002662  0.000716  0.001385 
 0.009236  0.002425  0.003179  0.003710  0.007173  0.003014  0.001456  0.700149  0.004657  0.062766  0.034609  0.003705  0.002207  0.002967  0.003311  0.006162  0.009210  0.134935  0.001136  0.003995 
 0.004805  0.001613  0.002508  0.003136  0.037896  0.002610  0.309142  0.004282  0.006120  0.009208  0.002821  0.004406  0.001965  0.004393  0.078000  0.005201  0.003661  0.004955  0.006245  0.507033 
 0.007132  0.001363  0.888432  0.028371  0.002159  0.004951  0.003743  0.003163  0.003841  0.004111  0.001647  0.023440  0.001990  0.003637  0.003479  0.007044  0.004092  0.004175  0.000844  0.002388 
 0.007715  0.002825  0.009737  0.008505  0.009382  0.005589  0.688412  0.004150  0.007098  0.037197  0.005057  0.026492  0.004617  0.108057  0.018114  0.013859  0.009595  0.006424  0.002913  0.024262 
 0.007228  0.002419  0.001026  0.001436  0.006204  0.001439  0.000645  0.378249  0.001593  0.310555  0.008874  0.001365  0.001150  0.001271  0.001277  0.002480  0.006162  0.263990  0.000634  0.002004 
 0.017613  0.001840  0.008499  0.031255  0.027163  0.821955  0.002701  0.003190  0.006660  0.028861  0.002078  0.009313  0.003211  0.003519  0.006057  0.012479  0.005222  0.004796  0.001110  0.002478 
 0.012933  0.001709  0.010693  0.008599  0.064966  0.589533  0.005542  0.004161  0.008899  0.006643  0.002637  0.064894  0.003268  0.057963  0.006705  0.012676  0.006941  0.005620  0.002859  0.122760 
 0.011150  0.001229  0.005337  0.003796  0.001274  0.936810  0.001712  0.001643  0.004026  0.002105  0.001130  0.005748  0.002224  0.002138  0.003795  0.007883  0.003238  0.002662  0.000716  0.001385 
 0.007156  0.003634  0.002520  0.003030  0.854939  0.002809  0.001789  0.011703  0.002727  0.046028  0.006608  0.002463  0.003043  0.001912  0.002284  0.007040  0.003622  0.010607  0.003899  0.022185 
 0.188701  0.002536  0.005237  0.004758  0.074416  0.005672  0.605292  0.004606  0.004171  0.009659  0.003600  0.012442  0.003127  0.013334  0.008339  0.011333  0.007453  0.006584  0.003453  0.025287 
 0.003126  0.001238  0.001442  0.001536  0.000942  0.002463  0.002724  0.001553  0.010720  0.002732  0.000855  0.002341  0.002057  0.003743  0.954420  0.002737  0.002157  0.001299  0.000824  0.001090 
 0.001177  0.000575  0.000799  0.000651  0.010620  0.001403  0.002368  0.001223  0.000830  0.002889  0.000747  0.001100  0.000889  0.000951  0.001092  0.001319  0.001017  0.001369  0.002122  0.966858 
 0.173881  0.004559  0.002500  0.002351  0.001788  0.011636  0.001323  0.002404  0.002675  0.003500  0.001755  0.005188  0.003884  0.002535  0.002920  0.741670  0.027372  0.006141  0.000552  0.001367 
 0.013197  0.002911  0.001213  0.001553  0.003395  0.003667  0.000733  0.034285  0.001737  0.015806  0.004409  0.001980  0.001630  0.001394  0.001529  0.007964  0.399389  0.501275  0.000432  0.001500 
 0.008736  0.001407  0.775405  0.056323  0.002216  0.028760  0.004567  0.003248  0.006031  0.004360  0.001767  0.027257  0.002599  0.005630  0.004368  0.010100  0.049338  0.004431  0.000835  0.002621 
 0.141603  0.002813  0.078461  0.099292  0.006404  0.068517  0.013640  0.009776  0.047671  0.017392  0.008220  0.026541  0.063719  0.085704  0.187202  0.089760  0.027921  0.015124  0.002021  0.008216 
 0.088606  0.056017  0.133166  0.210326  0.006111  0.015391  0.013073  0.009422  0.099354  0.016734  0.007898  0.025483  0.010680  0.139143  0.028374  0.035685  0.080147  0.014612  0.001929  0.007848 
 0.004066  0.001685  0.002785  0.003040  0.014246  0.003433  0.001897  0.003142  0.003287  0.013223  0.002922  0.002854  0.002010  0.003025  0.003932  0.003667  0.003277  0.004807  0.912886  0.009816 
 0.028438  0.007126  0.004594  0.008516  0.016338  0.008696  0.250274  0.102419  0.010353  0.168537  0.018646  0.007953  0.005736  0.008748  0.069234  0.017272  0.083120  0.170299  0.003333  0.010371 
 0.026515  0.005794  0.003530  0.005657  0.010129  0.005578  0.003475  0.167969  0.005975  0.126489  0.012115  0.050029  0.004397  0.004776  0.006037  0.010392  0.063548  0.480277  0.001875  0.005442 
 0.022431  0.001999  0.005976  0.007965  0.003055  0.006763  0.003195  0.005237  0.008624  0.009049  0.002647  0.004843  0.825375  0.006871  0.006607  0.015137  0.010114  0.051485  0.000699  0.001927 
 0.001543  0.000634  0.001822  0.001359  0.001788  0.001871  0.964981  0.000713  0.001090  0.002008  0.000740  0.003807  0.001236  0.004256  0.002681  0.002326  0.001656  0.001089  0.000607  0.003792 
 0.004960  0.002583  0.001915  0.002253  0.801769  0.002259  0.003865  0.007786  0.002262  0.020573  0.004469  0.002499  0.002251  0.002032  0.002243  0.005216  0.002925  0.007391  0.005041  0.115709 
 0.002410  0.000400  0.011890  0.964409  0.000643  0.001843  0.001040  0.001432  0.001277  0.001274  0.000540  0.002458  0.000645  0.003146  0.001143  0.001708  0.001452  0.001420  0.000270  0.000599 
 0.005687  0.001405  0.001921  0.002977  0.000998  0.002660  0.001815  0.003270  0.920150  0.003196  0.001539  0.003766  0.002124  0.002915  0.033907  0.003337  0.003856  0.002481  0.000753  0.001245 
 0.003186  0.001465  0.001339  0.001422  0.002571  0.001805  0.000918  0.008590  0.001862  0.019247  0.935892  0.001443  0.001421  0.001389  0.001257  0.002623  0.002760  0.006436  0.001371  0.003003 
 0.003856  0.001311  0.001061  0.001716  0.007685  0.001692  0.001140  0.015312  0.001898  0.925676  0.011130  0.001250  0.001719  0.002266  0.002306  0.002313  0.003280  0.011166  0.000963  0.002260 
 0.001177  0.000575  0.000799  0.000651  0.010620  0.001403  0.002368  0.001223  0.000830  0.002889  0.000747  0.001100  0.000889  0.000951  0.001092  0.001319  0.001017  0.001369  0.002122  0.966858 
 0.007132  0.001363  0.888432  0.028371  0.002159  0.004951  0.003743  0.003163  0.003841  0.004111  0.001647  0.023440  0.001990  0.003637  0.003479  0.007044  0.004092  0.004175  0.000844  0.002388 
 0.007325  0.001014  0.016375  0.011279  0.001511  0.009054  0.005046  0.001430  0.011498  0.002876  0.001168  0.326788  0.002842  0.569810  0.007545  0.012808  0.006608  0.002183  0.000527  0.002314 
 0.704554  0.007947  0.003326  0.004648  0.003487  0.117281  0.001870  0.005850  0.004239  0.008607  0.003967  0.004205  0.003235  0.003488  0.004167  0.083625  0
motif=4
starts: w=8, seq=0, l=865          
starts: w=8, seq=5, l=677          
starts: w=8, seq=10, l=681          
starts: w=11, seq=0, l=865          
starts: w=11, seq=5, l=677          
starts: w=11, seq=10, l=681          
starts: w=15, seq=0, l=865          
starts: w=15, seq=5, l=677          
starts: w=15, seq=10, l=681          
starts: w=21, seq=0, l=865          
starts: w=21, seq=5, l=677          
starts: w=21, seq=10, l=681          
starts: w=29, seq=0, l=865          
starts: w=29, seq=5, l=677          
starts: w=29, seq=10, l=681          
starts: w=41, seq=0, l=865          
starts: w=41, seq=5, l=677          
starts: w=41, seq=10, l=681          
starts: w=50, seq=0, l=865          
starts: w=50, seq=5, l=677          
starts: w=50, seq=10, l=681          

em: w=   8, psites=   2, iter=   0 
em: w=   8, psites=   2, iter=  10 
em: w=   8, psites=   4, iter=   0 
em: w=   8, psites=   4, iter=  10 
em: w=   8, psites=   4, iter=  20 
em: w=   8, psites=   4, iter=  30 
em: w=   8, psites=   4, iter=  40 
em: w=   8, psites=   8, iter=   0 
em: w=   8, psites=   8, iter=  10 
em: w=   8, psites=   8, iter=  20 
em: w=   8, psites=   8, iter=  30 
em: w=   8, psites=   8, iter=  40 
em: w=   8, psites=  12, iter=   0 
em: w=   8, psites=  12, iter=  10 
em: w=   8, psites=  12, iter=  20 
em: w=   8, psites=  12, iter=  30 
em: w=   8, psites=  12, iter=  40 
em: w=  11, psites=   2, iter=   0 
em: w=  11, psites=   2, iter=  10 
em: w=  11, psites=   2, iter=  20 
em: w=  11, psites=   2, iter=  30 
em: w=  11, psites=   2, iter=  40 
em: w=  11, psites=   4, iter=   0 
em: w=  11, psites=   8, iter=   0 
em: w=  11, psites=   8, iter=  10 
em: w=  11, psites=   8, iter=  20 
em: w=  11, psites=   8, iter=  30 
em: w=  11, psites=   8, iter=  40 
em: w=  11, psites=  12, iter=   0 
em: w=  11, psites=  12, iter=  10 
em: w=  11, psites=  12, iter=  20 
em: w=  15, psites=   2, iter=   0 
em: w=  15, psites=   2, iter=  10 
em: w=  15, psites=   2, iter=  20 
em: w=  15, psites=   2, iter=  30 
em: w=  15, psites=   2, iter=  40 
em: w=  15, psites=   4, iter=   0 
em: w=  15, psites=   8, iter=   0 
em: w=  15, psites=  12, iter=   0 
em: w=  15, psites=  12, iter=  10 
em: w=  15, psites=  12, iter=  20 
em: w=  15, psites=  12, iter=  30 
em: w=  15, psites=  12, iter=  40 
em: w=  21, psites=   2, iter=   0 
em: w=  21, psites=   4, iter=   0 
em: w=  21, psites=   8, iter=   0 
em: w=  21, psites=  12, iter=   0 
em: w=  29, psites=   2, iter=   0 
em: w=  29, psites=   2, iter=  10 
em: w=  29, psites=   2, iter=  20 
em: w=  29, psites=   2, iter=  30 
em: w=  29, psites=   2, iter=  40 
em: w=  29, psites=   4, iter=   0 
em: w=  29, psites=   8, iter=   0 
em: w=  29, psites=  12, iter=   0 
em: w=  41, psites=   2, iter=   0 
em: w=  41, psites=   4, iter=   0 
em: w=  41, psites=   8, iter=   0 
em: w=  41, psites=  12, iter=   0 
em: w=  50, psites=   2, iter=   0 
em: w=  50, psites=   4, iter=   0 
em: w=  50, psites=   8, iter=   0 
em: w=  50, psites=  12, iter=   0 .013685  0.018716  0.001025  0.002077 
 0.016981  0.003043  0.006830  0.054387  0.005840  0.005684  0.017169  0.012445  0.014577  0.111826  0.039035  0.010238  0.005859  0.606584  0.014422  0.013354  0.012104  0.014399  0.030772  0.004450 
 0.043028  0.002571  0.001860  0.003710  0.013498  0.002551  0.002157  0.065027  0.004057  0.783467  0.021416  0.002516  0.003167  0.004734  0.004787  0.004885  0.006970  0.023962  0.001663  0.003976 
 0.131607  0.004000  0.002031  0.003855  0.013402  0.004059  0.002661  0.095402  0.004418  0.465187  0.134915  0.003462  0.003208  0.004414  0.004607  0.007750  0.011762  0.095710  0.002010  0.005538 
 0.088478  0.004424  0.018273  0.032778  0.065952  0.013567  0.011417  0.021387  0.034975  0.028604  0.066206  0.074245  0.009339  0.078948  0.131190  0.030829  0.135645  0.081928  0.002644  0.069170 
 0.557622  0.007927  0.003570  0.005729  0.007318  0.014356  0.002714  0.022857  0.005789  0.069692  0.008555  0.004722  0.003306  0.004545  0.005383  0.028236  0.110396  0.131431  0.001640  0.004213 
 0.006075  0.001969  0.002433  0.003148  0.115577  0.002682  0.010637  0.006466  0.003367  0.153086  0.004151  0.003641  0.002237  0.003262  0.003757  0.005740  0.003975  0.006679  0.006765  0.654354






Time 75.07 secs.

P N
MOTIF 4 width = 41 sites = 11 llr = 809 E-value = 3.8e-107

NAME	START	P-VALUE				SITES
			Simplified	A	:	2	1	:	:	1	5	:	:	1	:	1	1	:	1	:	:	:	:	:	:	2	2	:	:	1	:	2	:	3	5	:	6	:	5	2	1	2	:	:	2
			pos.-specific	C	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	2	:	1	:	:	1	:	:	:
			probability	D	:	1	:	:	:	1	:	:	1	:	:	:	:	:	:	:	a	5	:	:	:	:	3	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	2	3
			matrix	E	:	2	:	:	:	3	:	:	3	2	:	3	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	1	:	:	:	:	:	1	4
				F	:	:	:	:	4	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	2	:	:
				G	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	1	:	:	9	:	:	:	1	4	:	:	:	:	3	:	:	:	4	:
				H	:	:	:	:	1	:	:	:	:	1	:	:	:	:	5	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	1	1	1	:	:	:	:	1
				I	:	:	3	:	:	:	2	:	:	:	:	:	:	:	:	1	:	:	:	4	2	:	:	:	:	:	:	:	6	:	:	:	:	:	:	:	:	2	:	:	:
				K	1	1	5	:	:	1	:	:	1	3	:	:	4	:	:	:	:	:	9	:	:	:	:	:	:	:	:	:	:	:	:	:	:	3	:	:	4	:	:	1	:
				L	1	:	:	9	5	:	:	:	3	:	:	:	:	:	1	4	:	:	:	:	5	:	:	:	:	:	9	:	3	:	:	8	:	:	2	:	:	:	5	:	:
				M	:	:	:	1	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	2	:	:	:	:	:	:	1	5	:	:	:	:	:	1	:	:	:	:	:	:	:
				N	1	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	9	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:
				P	:	:	:	:	:	:	:	:	:	:	:	5	:	a	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				Q	:	1	1	:	:	1	:	:	1	2	:	:	2	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	1	:	:	1	1
				R	7	4	:	:	:	1	1	a	:	1	a	:	1	:	:	2	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	2	:	:	2	:	:	1	:
				S	:	:	:	:	:	:	:	:	1	:	:	:	1	:	1	:	:	2	:	:	:	:	5	:	:	:	:	:	:	3	1	:	1	:	:	3	:	:	1	1	:
				T	:	:	:	:	:	:	1	:	1	:	:	1	:	:	:	1	:	2	1	:	:	6	:	:	:	:	:	1	:	2	:	:	:	:	1	:	:	:	1	:	:
				V	:	:	1	:	:	2	1	:	:	1	:	1	:	:	:	3	:	:	:	5	2	1	:	:	:	:	:	3	1	:	:	:	1	1	:	:	1	5	:	:	:
				W	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	a	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:
				Y	:	:	:	:	:	:	:	:	:	:	:	:	1	:	1	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	1	:	1	:	2	:	:	2	:	:
.
			bits	6.3
				5.6
				5.0
				4.4
			Information	3.8
			content	3.1
			(106.1 bits)	2.5
				1.9
				1.3
				0.6
				0.0
.
			Multilevel		`R`	`R`	`K`	`L`	`L`	`E`	`A`	`R`	`E`	`K`	`R`	`P`	`K`	`P`	`H`	`L`	`D`	`D`	`K`	`V`	`L`	`T`	`S`	`W`	`N`	`G`	`L`	`M`	`I`	`A`	`A`	`L`	`A`	`K`	`A`	`G`	`K`	`V`	`L`	`G`	`E`
			consensus				`I`		`F`				`L`			`E`				`V`				`I`			`D`					`V`	`L`	`S`	`G`					`S`					`D`
			sequence


.

D.radiodaurans	409	3.66e-35	`DDAAQRLQAA`		`R`	`A`	`K`	`L`	`F`	`A`	`A`	`R`	`Q`	`V`	`R`	`P`	`Q`	`P`	`H`	`T`	`D`	`D`	`K`	`V`	`L`	`T`	`S`	`W`	`N`	`G`	`L`	`V`	`L`	`A`	`A`	`L`	`A`	`D`	`A`	`A`	`R`	`I`	`L`	`G`	`E`	`EKYLDLARRN`
B.subtilis	398	5.26e-35	`KELSLKLEDA`		`R`	`Q`	`Q`	`L`	`L`	`K`	`T`	`R`	`E`	`E`	`R`	`T`	`Y`	`P`	`H`	`V`	`D`	`D`	`K`	`V`	`L`	`T`	`S`	`W`	`N`	`A`	`L`	`M`	`I`	`A`	`G`	`L`	`A`	`K`	`A`	`A`	`K`	`V`	`Y`	`Q`	`E`	`PKYLSLAKDA`
A.thaliana	573	5.93e-35	`EKYQEILGEC`		`R`	`R`	`K`	`L`	`F`	`D`	`V`	`R`	`L`	`K`	`R`	`P`	`K`	`P`	`H`	`L`	`D`	`D`	`K`	`I`	`I`	`V`	`S`	`W`	`N`	`G`	`L`	`V`	`I`	`S`	`S`	`F`	`A`	`R`	`A`	`S`	`K`	`I`	`L`	`K`	`A`	`EPESTKYYFP`
A.aeolicus	403	9.40e-33	`KELKEKLERI`		`R`	`K`	`K`	`L`	`F`	`E`	`A`	`R`	`E`	`K`	`R`	`V`	`K`	`P`	`L`	`R`	`D`	`E`	`K`	`I`	`L`	`T`	`D`	`W`	`N`	`G`	`L`	`T`	`I`	`A`	`A`	`L`	`S`	`Y`	`A`	`G`	`K`	`V`	`F`	`G`	`E`	`KEWIDLAKGA`
M.thermoautotrophicum	395	2.69e-32	`DELNERIEEA`		`R`	`R`	`V`	`L`	`L`	`E`	`R`	`R`	`L`	`E`	`R`	`E`	`A`	`P`	`S`	`V`	`D`	`D`	`K`	`V`	`L`	`T`	`D`	`W`	`N`	`G`	`L`	`M`	`I`	`G`	`A`	`L`	`A`	`R`	`C`	`S`	`R`	`V`	`L`	`D`	`H`	`DESLRAAEGC`
A.pernix	393	4.12e-31	`DRAWEVLEES`		`R`	`R`	`I`	`L`	`L`	`R`	`I`	`R`	`S`	`R`	`R`	`E`	`K`	`P`	`G`	`V`	`D`	`D`	`K`	`V`	`L`	`T`	`D`	`W`	`N`	`G`	`M`	`M`	`L`	`H`	`A`	`L`	`A`	`H`	`L`	`Y`	`W`	`V`	`S`	`R`	`D`	`PEVLGVAKSL`
H.sapiens	485	9.90e-31	`EAVRTLLNSG`		`L`	`E`	`K`	`L`	`F`	`Q`	`A`	`R`	`K`	`H`	`R`	`P`	`K`	`P`	`H`	`L`	`D`	`S`	`K`	`M`	`L`	`A`	`A`	`W`	`N`	`G`	`L`	`M`	`V`	`S`	`G`	`Y`	`A`	`V`	`T`	`G`	`A`	`V`	`L`	`G`	`Q`	`DRLINYATNG`
D.melanogaster	500	5.48e-30	`DRFKKLLATT`		`N`	`D`	`I`	`L`	`H`	`V`	`I`	`R`	`D`	`K`	`R`	`P`	`R`	`P`	`H`	`L`	`D`	`T`	`K`	`I`	`I`	`C`	`A`	`W`	`N`	`G`	`L`	`V`	`L`	`S`	`G`	`L`	`C`	`K`	`L`	`G`	`N`	`C`	`Y`	`S`	`A`	`NREQYMQTAK`
C.elegans	435	6.02e-30	`AELKKGIDEA`		`K`	`E`	`I`	`L`	`W`	`N`	`A`	`R`	`T`	`Q`	`R`	`P`	`S`	`P`	`H`	`L`	`D`	`S`	`K`	`M`	`V`	`T`	`S`	`W`	`Q`	`G`	`L`	`A`	`I`	`T`	`G`	`L`	`V`	`K`	`A`	`Y`	`Q`	`A`	`T`	`E`	`E`	`TKYLDRAEKC`
M.tuberculosis	386	1.39e-29	`PDDAARLDRV`		`R`	`A`	`A`	`L`	`L`	`V`	`A`	`R`	`L`	`A`	`R`	`A`	`Q`	`P`	`A`	`R`	`D`	`D`	`K`	`V`	`V`	`T`	`S`	`W`	`N`	`G`	`L`	`A`	`I`	`T`	`A`	`L`	`A`	`E`	`A`	`S`	`V`	`A`	`L`	`D`	`D`	`PALAHAARRC`
A.fulgidus	388	2.88e-29	`EEVERAVNSA`		`R`	`R`	`K`	`M`	`L`	`E`	`F`	`R`	`E`	`Q`	`R`	`E`	`M`	`P`	`Y`	`I`	`D`	`T`	`T`	`I`	`Y`	`A`	`G`	`W`	`N`	`G`	`L`	`M`	`I`	`E`	`A`	`L`	`C`	`M`	`H`	`H`	`K`	`V`	`F`	`G`	`D`	`NWSLEMAEKT`

Motif 4 block diagrams

Name

Lowest
p-value

Motifs

D.radiodaurans

3.7e-35

B.subtilis

5.3e-35

A.thaliana

5.9e-35

A.aeolicus

9.4e-33

M.thermoautotrophicum

2.7e-32

A.pernix

4.1e-31

H.sapiens

9.9e-31

D.melanogaster

5.5e-30

C.elegans

6e-30

M.tuberculosis

1.4e-29

A.fulgidus

2.9e-29

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775	800	825	850

Motif 4 in BLOCKS format

BL   MOTIF 4 width=41 seqs=11
D.radiodaurans           (  409) RAKLFAARQVRPQPHTDDKVLTSWNGLVLAALADAARILGE  1 
B.subtilis               (  398) RQQLLKTREERTYPHVDDKVLTSWNALMIAGLAKAAKVYQE  1 
A.thaliana               (  573) RRKLFDVRLKRPKPHLDDKIIVSWNGLVISSFARASKILKA  1 
A.aeolicus               (  403) RKKLFEAREKRVKPLRDEKILTDWNGLTIAALSYAGKVFGE  1 
M.thermoautotrophicum    (  395) RRVLLERRLEREAPSVDDKVLTDWNGLMIGALARCSRVLDH  1 
A.pernix                 (  393) RRILLRIRSRREKPGVDDKVLTDWNGMMLHALAHLYWVSRD  1 
H.sapiens                (  485) LEKLFQARKHRPKPHLDSKMLAAWNGLMVSGYAVTGAVLGQ  1 
D.melanogaster           (  500) NDILHVIRDKRPRPHLDTKIICAWNGLVLSGLCKLGNCYSA  1 
C.elegans                (  435) KEILWNARTQRPSPHLDSKMVTSWQGLAITGLVKAYQATEE  1 
M.tuberculosis           (  386) RAALLVARLARAQPARDDKVVTSWNGLAITALAEASVALDD  1 
A.fulgidus               (  388) RRKMLEFREQREMPYIDTTIYAGWNGLMIEALCMHHKVFGD  1 
//

Motif 4 position-specific scoring matrix

log-odds matrix: alength= 20 w= 41 n= 7557 bayes= 9.32063 E= 3.8e-107 
  -358   -262   -423   -360   -478   -397   -211   -339     56   -126   -326     44   -366   -126    368   -308   -286   -395   -358   -397 
    65   -266     47    114   -328   -254   -145   -239     91   -293   -195    -64   -243    144    212   -115   -111   -234   -355   -266 
   -11   -175   -263   -202   -244   -297   -186    240    272   -200   -124   -132   -296    134   -112   -168   -126     58   -308   -248 
  -376   -252   -526   -465   -169   -506   -391    -49   -394    302    137   -388   -408   -291   -383   -393   -293   -155   -345   -336 
  -489   -323   -582   -587    294   -545    153   -238   -488    201   -234   -369   -518   -376   -468   -439   -397   -317    223      7 
    -5   -224     38    138   -284   -220   -110   -204     91   -258   -158    132   -212    143     47    -77    -73    103   -316   -226 
   213    -68   -378   -333     57   -263   -257    184   -258   -129    -57   -216   -321   -210      2   -142     70     75   -257   -214 
  -488   -338   -540   -570   -556   -486   -339   -466   -231   -522   -481   -375   -452   -309    401   -449   -439   -551   -442   -513 
  -144   -236     42    145   -295   -228   -120   -212     89     81   -168    -38   -220    143   -114     52     82   -208   -327   -237 
    -7   -231   -142     92   -295   -231    124   -212    202   -265   -166    -40   -224    215     56    -88    -84     21   -322   -234 
  -488   -338   -540   -570   -556   -486   -339   -466   -231   -522   -481   -375   -452   -309    401   -449   -439   -551   -442   -513 
   -40   -251   -255     95   -364   -314   -276   -264   -206   -328   -277   -213    356   -161   -275   -179     33    -13   -436   -386 
    -7   -231   -148   -101   -295   -233   -118   -209    236   -264    138    -42   -227    216     58     52    -86   -208   -322     71 
  -362   -395   -470   -485   -520   -456   -448   -454   -414   -499   -474   -410    434   -371   -458   -356   -368   -453   -559   -549 
  -142   -207   -253   -304   -221   -121    452   -288   -292   -145   -210    -21   -323     -1   -173    -62   -205   -288   -258     36 
  -196   -105   -424   -372   -160   -337   -275    143   -286    163    -48   -243   -334   -233    114   -219     84    200   -266   -219 
  -369   -324    387   -149   -436   -385   -293   -363   -379   -463   -387    -42   -457   -313   -409   -313   -347   -383   -438   -400 
  -299   -339    322     22   -454   -272   -231   -385   -218   -458   -375    -13   -357   -161   -320     97    133   -382   -478   -382 
  -382   -305   -480   -450   -535   -461   -376   -341    408   -481   -377   -285   -434   -315    -62   -399   -165   -438   -441   -478 
  -354   -229   -597   -585   -320   -565   -565    322   -517   -191    263   -460   -541   -489   -569   -468   -280    283   -522   -449 
  -320   -209   -532   -480   -188   -470   -391    199   -405    242    -57   -370   -426   -322   -410   -359   -243    137   -348     74 
    68    234   -432   -466   -383   -309   -387   -210   -358   -372   -248   -207   -368   -293   -382    -69    374     34   -435   -427 
    94   -209    200   -293   -476     33   -281   -427   -283   -495   -402    -68   -351   -237   -365    271   -188   -356   -514   -428 
  -450   -294   -445   -471   -164   -438   -391   -364   -401   -295   -304   -346   -455   -339   -391   -407   -379   -363    569   -196 
  -391   -258   -224   -432   -375   -350   -109   -261   -289   -420   -320    478   -370    -98   -351   -151   -211   -348   -354   -358 
  -103   -278   -292   -379   -462    362   -353   -397   -312   -508   -379   -183   -391   -332   -338   -229   -315   -383   -413   -427 
  -376   -252   -526   -465   -169   -506   -391    -49   -394    302    137   -388   -408   -291   -383   -393   -293   -155   -345   -336 
    82   -127   -457   -414   -216   -329   -326    -11   -336   -165    389   -279   -361   -280   -358   -217     91    208   -322   -274 
  -345   -245   -461   -474   -264   -484   -457    402   -385     65    -84   -341   -466   -370   -447   -363   -248    114   -413   -349 
   125   -194   -144     16   -302     -4    119   -221    -56   -282   -183    -37   -239    -34   -139    182    161   -210   -338   -253 
   252   -137   -489   -514   -476    215   -467   -401   -478   -482   -378   -321   -372   -378   -470     69   -196   -286   -512   -516 
  -393   -264   -529   -478     57   -508   -321    -79   -403    292    -49   -374   -421   -300   -391   -395   -308   -181   -267     68 
   291    248   -384   -364   -318   -178   -355   -220   -316   -304   -209   -271   -398   -286   -341     23   -158     -5   -364   -375 
  -135   -218     35     29   -277   -218    122   -198    196   -253    134    -27   -211      6    120    -74    -70     19   -311     68 
   275    172   -366   -339   -263   -189     32   -139   -281    -27   -155   -244   -374   -250   -312    -68     13    -89   -327   -314 
    87   -192   -200   -224   -299    166    140   -265   -164   -343   -253    -80   -302   -137   -242    191   -149   -252   -380    194 
   -11   -248   -176   -124   -319   -255   -132   -227    246   -281   -184    132   -249    145    136   -115   -107     24    176   -255 
    -2    147   -397   -386   -289   -403   -332    158   -341   -217   -178   -311   -344   -318   -342   -304   -139    346   -416   -402 
  -232   -141   -414   -377    174   -360   -195    -48   -300    192    -79   -248   -347   -241   -317     21     71    -90   -196    213 
  -151   -237    117     35   -299    175   -121   -220     89   -274   -175    -27   -225    142     47     53    -87   -216   -331   -240 
    68   -450    194    221   -497   -338    129   -355   -150   -412   -319   -161   -312    144   -282   -228   -225   -330   -524   -420

Motif 4 position-specific probability matrix

letter-probability matrix: alength= 20 w= 41 n= 7557 E= 3.8e-107 
 0.007688  0.002096  0.003236  0.006562  0.001612  0.004576  0.006634  0.003739  0.078479  0.042519  0.002507  0.042533  0.003738  0.013266  0.759554  0.007278  0.006234  0.003840  0.001474  0.002436 
 0.144021  0.002039  0.084050  0.175313  0.004564  0.012328  0.010453  0.007474  0.099889  0.013376  0.006245  0.020089  0.008732  0.086367  0.257036  0.027701  0.021037  0.011747  0.001503  0.006038 
 0.085592  0.003839  0.009796  0.019610  0.008208  0.009123  0.007868  0.207641  0.350434  0.025564  0.010212  0.012589  0.006066  0.080488  0.027239  0.019249  0.018935  0.088616  0.002079  0.006854 
 0.006786  0.002243  0.001583  0.003173  0.013775  0.002148  0.001901  0.027970  0.003469  0.825922  0.062138  0.002129  0.002781  0.004220  0.004169  0.004037  0.005944  0.020271  0.001613  0.003728 
 0.003109  0.001372  0.001075  0.001361  0.340297  0.001635  0.082586  0.007526  0.001801  0.411077  0.004752  0.002425  0.001302  0.002353  0.002308  0.002939  0.002894  0.006608  0.082484  0.040098 
 0.088758  0.002726  0.079146  0.208401  0.006222  0.015527  0.013283  0.009570  0.099918  0.017022  0.008041  0.078584  0.010824  0.085816  0.082005  0.036189  0.027234  0.120776  0.001967  0.007990 
 0.402104  0.008081  0.004432  0.007938  0.066037  0.011582  0.004820  0.140440  0.008888  0.041626  0.016172  0.007016  0.005080  0.007389  0.060148  0.023052  0.073821  0.099712  0.002964  0.008699 
 0.003126  0.001238  0.001442  0.001536  0.000942  0.002463  0.002724  0.001553  0.010720  0.002732  0.000855  0.002341  0.002057  0.003743  0.954420  0.002737  0.002157  0.001299  0.000824  0.001090 
 0.033892  0.002523  0.081348  0.217626  0.005767  0.014679  0.012387  0.009013  0.098279  0.178718  0.007523  0.024138  0.010278  0.085816  0.026915  0.088097  0.079743  0.014027  0.001821  0.007412 
 0.087657  0.002597  0.022622  0.151505  0.005752  0.014405  0.067616  0.009045  0.215465  0.016213  0.007601  0.023849  0.009962  0.141409  0.087437  0.033357  0.025336  0.068753  0.001894  0.007526 
 0.003126  0.001238  0.001442  0.001536  0.000942  0.002463  0.002724  0.001553  0.010720  0.002732  0.000855  0.002341  0.002057  0.003743  0.954420  0.002737  0.002157  0.001299  0.000824  0.001090 
 0.069832  0.002260  0.010335  0.154188  0.003555  0.008083  0.004217  0.006279  0.012766  0.010535  0.003542  0.007160  0.555564  0.010373  0.008780  0.017827  0.057056  0.054156  0.000858  0.002635 
 0.087461  0.002612  0.021746  0.039751  0.005761  0.014179  0.012635  0.009198  0.272701  0.016316  0.062822  0.023456  0.009780  0.141540  0.088424  0.087987  0.025013  0.014001  0.001896  0.062721 
 0.007507  0.000833  0.002329  0.002772  0.001213  0.003031  0.001278  0.001681  0.003014  0.003215  0.000898  0.001827  0.952984  0.002427  0.002472  0.005202  0.003528  0.002572  0.000367  0.000849 
 0.034371  0.003075  0.010477  0.009679  0.009571  0.030972  0.653745  0.005335  0.007026  0.037417  0.005604  0.027132  0.005023  0.031613  0.017849  0.040083  0.010903  0.008034  0.002940  0.049150 
 0.023651  0.006216  0.003214  0.006037  0.014655  0.006904  0.004250  0.105798  0.007306  0.315183  0.017265  0.005808  0.004648  0.006311  0.130024  0.013452  0.080934  0.237156  0.002787  0.008400 
 0.007132  0.001363  0.888432  0.028371  0.002159  0.004951  0.003743  0.003163  0.003841  0.004111  0.001647  0.023440  0.001990  0.003637  0.003479  0.007044  0.004092  0.004175  0.000844  0.002388 
 0.011586  0.001227  0.563897  0.092689  0.001913  0.010831  0.005768  0.002729  0.011722  0.004277  0.001787  0.028771  0.003979  0.010416  0.006458  0.120595  0.113811  0.004192  0.000642  0.002710 
 0.006509  0.001555  0.002177  0.003515  0.001088  0.002931  0.002107  0.003689  0.898820  0.003629  0.001761  0.004356  0.002334  0.003579  0.038526  0.003885  0.014475  0.002844  0.000828  0.001393 
 0.007897  0.002630  0.000968  0.001382  0.004825  0.001422  0.000570  0.365039  0.001471  0.027131  0.149168  0.001295  0.001109  0.001075  0.001148  0.002405  0.006524  0.421761  0.000473  0.001706 
 0.010027  0.003032  0.001515  0.002856  0.012075  0.002747  0.001899  0.155777  0.003212  0.546737  0.016261  0.002413  0.002454  0.003418  0.003453  0.005121  0.008404  0.153229  0.001580  0.063791 
 0.147984  0.065556  0.003036  0.003154  0.003119  0.008384  0.001956  0.009165  0.004445  0.007727  0.004323  0.007453  0.003684  0.004156  0.004185  0.038108  0.605522  0.075202  0.000867  0.001975 
 0.176283  0.003027  0.242147  0.010487  0.001641  0.089645  0.004069  0.002038  0.007493  0.003297  0.001485  0.019570  0.004127  0.006136  0.004702  0.404025  0.012341  0.005019  0.000499  0.001971 
 0.004066  0.001685  0.002785  0.003040  0.014246  0.003433  0.001897  0.003142  0.003287  0.013223  0.002922  0.002854  0.002010  0.003025  0.003932  0.003667  0.003277  0.004807  0.912886  0.009816 
 0.006138  0.002159  0.012806  0.004005  0.003302  0.006298  0.013424  0.006442  0.007186  0.005541  0.002612  0.863126  0.003621  0.016056  0.005184  0.021550  0.010497  0.005335  0.001514  0.003204 
 0.044947  0.001875  0.008016  0.005781  0.001808  0.876042  0.002475  0.002497  0.006103  0.003013  0.001743  0.008815  0.003147  0.003190  0.005671  0.012619  0.005100  0.004170  0.001008  0.001982 
 0.006786  0.002243  0.001583  0.003173  0.013775  0.002148  0.001901  0.027970  0.003469  0.825922  0.062138  0.002129  0.002781  0.004220  0.004169  0.004037  0.005944  0.020271  0.001613  0.003728 
 0.162138  0.005362  0.002558  0.004529  0.009924  0.007332  0.002973  0.036358  0.005167  0.032475  0.356024  0.004528  0.003853  0.004576  0.004960  0.013661  0.084845  0.251118  0.001888  0.005733 
 0.008437  0.002369  0.002494  0.002980  0.007152  0.002498  0.001204  0.636897  0.003682  0.160204  0.013484  0.002954  0.001869  0.002451  0.002673  0.004964  0.008124  0.131158  0.001005  0.003400 
 0.219716  0.003356  0.022296  0.089398  0.005468  0.069752  0.065032  0.008486  0.036038  0.014437  0.006767  0.024272  0.009019  0.025154  0.022601  0.217846  0.138195  0.013840  0.001690  0.006638 
 0.528300  0.004986  0.002049  0.002256  0.001642  0.317586  0.001122  0.002434  0.001929  0.003608  0.001755  0.003382  0.003578  0.002309  0.002283  0.09
motif=5
starts: w=8, seq=0, l=865          
starts: w=8, seq=5, l=677          
starts: w=8, seq=10, l=681          
starts: w=11, seq=0, l=865          
starts: w=11, seq=5, l=677          
starts: w=11, seq=10, l=681          
starts: w=15, seq=0, l=865          
starts: w=15, seq=5, l=677          
starts: w=15, seq=10, l=681          
starts: w=21, seq=0, l=865          
starts: w=21, seq=5, l=677          
starts: w=21, seq=10, l=681          
starts: w=29, seq=0, l=865          
starts: w=29, seq=5, l=677          
starts: w=29, seq=10, l=681          
starts: w=41, seq=0, l=865          
starts: w=41, seq=5, l=677          
starts: w=41, seq=10, l=681          
starts: w=50, seq=0, l=865          
starts: w=50, seq=5, l=677          
starts: w=50, seq=10, l=681          

em: w=   8, psites=   2, iter=   0 
em: w=   8, psites=   2, iter=  10 
em: w=   8, psites=   2, iter=  20 
em: w=   8, psites=   2, iter=  30 
em: w=   8, psites=   2, iter=  40 
em: w=   8, psites=   4, iter=   0 
em: w=   8, psites=   4, iter=  10 
em: w=   8, psites=   4, iter=  20 
em: w=   8, psites=   4, iter=  30 
em: w=   8, psites=   4, iter=  40 
em: w=   8, psites=   8, iter=   0 
em: w=   8, psites=   8, iter=  10 
em: w=   8, psites=   8, iter=  20 
em: w=   8, psites=   8, iter=  30 
em: w=   8, psites=   8, iter=  40 
em: w=   8, psites=  12, iter=   0 
em: w=   8, psites=  12, iter=  10 
em: w=   8, psites=  12, iter=  20 
em: w=   8, psites=  12, iter=  30 
em: w=   8, psites=  12, iter=  40 
em: w=  11, psites=   2, iter=   0 
em: w=  11, psites=   2, iter=  10 
em: w=  11, psites=   2, iter=  20 
em: w=  11, psites=   2, iter=  30 
em: w=  11, psites=   2, iter=  40 
em: w=  11, psites=   4, iter=   0 
em: w=  11, psites=   8, iter=   0 
em: w=  11, psites=   8, iter=  10 
em: w=  11, psites=   8, iter=  20 
em: w=  11, psites=   8, iter=  30 
em: w=  11, psites=   8, iter=  40 
em: w=  11, psites=  12, iter=   0 
em: w=  11, psites=  12, iter=  10 
em: w=  11, psites=  12, iter=  20 
em: w=  15, psites=   2, iter=   0 
em: w=  15, psites=   2, iter=  10 
em: w=  15, psites=   2, iter=  20 
em: w=  15, psites=   2, iter=  30 
em: w=  15, psites=   2, iter=  40 
em: w=  15, psites=   4, iter=   0 
em: w=  15, psites=   4, iter=  10 
em: w=  15, psites=   4, iter=  20 
em: w=  15, psites=   4, iter=  30 
em: w=  15, psites=   4, iter=  40 
em: w=  15, psites=   8, iter=   0 
em: w=  15, psites=  12, iter=   0 
em: w=  15, psites=  12, iter=  10 
em: w=  15, psites=  12, iter=  20 
em: w=  15, psites=  12, iter=  30 
em: w=  15, psites=  12, iter=  40 
em: w=  21, psites=   2, iter=   0 
em: w=  21, psites=   4, iter=   0 
em: w=  21, psites=   8, iter=   0 
em: w=  21, psites=  12, iter=   0 
em: w=  29, psites=   2, iter=   0 
em: w=  29, psites=   2, iter=  10 
em: w=  29, psites=   2, iter=  20 
em: w=  29, psites=   2, iter=  30 
em: w=  29, psites=   2, iter=  40 
em: w=  29, psites=   4, iter=   0 
em: w=  29, psites=   8, iter=   0 
em: w=  29, psites=  12, iter=   0 
em: w=  41, psites=   2, iter=   0 
em: w=  41, psites=   4, iter=   0 
em: w=  41, psites=   8, iter=   0 
em: w=  41, psites=  12, iter=   0 
em: w=  41, psites=  12, iter=  10 
em: w=  41, psites=  12, iter=  20 
em: w=  41, psites=  12, iter=  30 
em: w=  41, psites=  12, iter=  40 
em: w=  50, psites=   2, iter=   0 
em: w=  50, psites=   4, iter=   0 
em: w=  50, psites=   8, iter=   0 
em: w=  50, psites=  12, iter=   0 9376  0.011651  0.008175  0.000508  0.001072 
 0.006021  0.002078  0.001549  0.002897  0.065753  0.002113  0.003077  0.022668  0.003245  0.770434  0.017134  0.002343  0.002544  0.003963  0.003941  0.003975  0.005353  0.016934  0.002769  0.061208 
 0.690133  0.071871  0.004247  0.006396  0.004890  0.020768  0.002429  0.008556  0.005944  0.012444  0.005647  0.004803  0.002995  0.004363  0.005560  0.072017  0.015199  0.057480  0.001413  0.002845 
 0.036250  0.002840  0.077554  0.097468  0.006533  0.015774  0.066312  0.009941  0.206890  0.017608  0.060913  0.026070  0.010944  0.033149  0.135919  0.036890  0.027833  0.067898  0.002048  0.061168 
 0.619601  0.042435  0.004814  0.007633  0.007163  0.019251  0.035752  0.014922  0.007589  0.084544  0.008248  0.005781  0.003530  0.005624  0.006802  0.038440  0.049642  0.032057  0.001828  0.004345 
 0.168706  0.003409  0.015188  0.016875  0.005592  0.225401  0.075084  0.006270  0.016993  0.009494  0.004165  0.018097  0.005799  0.012262  0.011032  0.231750  0.016121  0.010319  0.001265  0.146176 
 0.085348  0.002315  0.017950  0.033716  0.004858  0.012240  0.011395  0.008130  0.291448  0.014561  0.006706  0.078303  0.008370  0.086582  0.152304  0.027773  0.021532  0.070244  0.059708  0.006518 
 0.091137  0.035687  0.003878  0.005504  0.005994  0.004391  0.002862  0.116977  0.004999  0.022734  0.006996  0.003639  0.004357  0.003516  0.005521  0.007481  0.017295  0.653691  0.000989  0.002353 
 0.018407  0.004857  0.003452  0.005865  0.148085  0.005916  0.007399  0.028207  0.006659  0.386059  0.013932  0.005633  0.004245  0.005991  0.006595  0.071379  0.074134  0.031739  0.004522  0.166925 
 0.032376  0.002504  0.136428  0.101552  0.005577  0.240671  0.012353  0.008547  0.098582  0.015221  0.007159  0.026044  0.009902  0.085082  0.082008  0.088850  0.024846  0.013259  0.001777  0.007260 
 0.147974  0.000571  0.233064  0.368498  0.001419  0.006848  0.069876  0.003341  0.018778  0.005857  0.002640  0.010300  0.005412  0.086256  0.008373  0.012641  0.009556  0.006043  0.000465  0.002087






Time 103.20 secs.

P N
MOTIF 5 width = 42 sites = 11 llr = 794 E-value = 1.4e-090

NAME	START	P-VALUE				SITES
			Simplified	A	3	:	:	:	:	:	9	:	:	3	1	3	:	1	3	:	:	:	5	:	:	:	:	3	1	:	:	2	8	:	1	:	1	:	:	2	1	1	:	:	:	:
			pos.-specific	C	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	1	:	:	:	:	:	:
			probability	D	:	:	:	5	a	:	:	:	:	:	:	:	:	:	5	:	:	1	:	:	:	5	1	1	:	:	:	:	:	:	:	:	:	5	1	:	3	2	2	:	1	7
			matrix	E	:	:	:	5	:	:	:	:	:	:	:	:	:	:	2	:	:	5	:	:	:	2	1	4	:	:	3	1	:	:	4	:	:	3	:	:	:	1	:	:	:	:
				F	:	5	:	:	:	:	:	6	2	:	:	:	:	:	:	:	2	:	:	:	1	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	8	:	:
				G	7	:	:	:	:	:	:	:	:	1	:	7	:	:	:	:	:	:	:	2	4	1	1	1	:	:	1	:	:	:	1	:	:	:	1	:	:	:	:	:	1	1
				H	:	:	:	:	:	2	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	1	:	2	:	:	:	:	:	:	:	:	:	:	:	2	1	:	:
				I	:	1	1	:	:	:	1	:	:	5	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	1	:	:	:	2	:	1	:	:	4	:	3	:	:	:	:	:
				K	:	1	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	1	:	:	:	1	:	1	:	:	2	4	:	3	3	:	:	2	:	:	:	4	2	:	:	:
				L	:	2	7	:	:	:	:	1	5	1	1	:	9	7	:	8	:	:	1	:	3	:	2	:	:	9	:	:	:	2	:	9	1	:	:	1	:	:	4	1	:	:
				M	:	1	:	:	:	:	:	1	:	:	:	:	:	1	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	2	:	:	:	:	:	:
				N	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	1	:	:	1
				P	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				Q	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	2	:	:	2	:	:	:	:	:	1	:	:	:	:	:	5	:	:	4	:	:	:	:	:	:
				R	:	:	:	:	:	:	:	:	:	:	2	:	:	:	:	:	:	:	:	:	:	2	:	:	:	:	1	:	:	1	1	:	:	:	:	:	2	1	:	:	1	:
				S	:	:	2	:	:	:	:	:	:	:	1	:	:	:	1	:	:	:	:	3	1	:	2	1	:	:	:	:	:	:	1	:	:	:	1	:	:	1	:	:	:	1
				T	:	:	:	:	:	:	:	:	1	:	1	:	:	:	:	:	:	2	1	5	:	:	1	:	:	:	1	:	:	1	:	:	2	:	4	:	:	:	:	:	:	:
				V	:	:	:	:	:	:	:	:	1	1	:	:	:	1	:	:	:	:	2	1	:	:	1	:	1	:	:	:	1	1	:	:	1	:	:	1	2	1	:	:	:	:
				W	:	:	:	:	:	:	:	:	:	:	3	:	:	:	:	:	:	:	:	:	:	:	:	:	3	:	:	4	:	:	:	:	1	:	:	:	:	:	:	:	7	:
				Y	:	:	:	:	:	8	:	2	1	:	:	:	1	:	:	1	8	:	:	:	:	:	:	:	5	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
.
			bits	6.3
				5.6
				5.0
				4.4
			Information	3.8
			content	3.1
			(104.1 bits)	2.5
				1.9
				1.3
				0.6
				0.0
.
			Multilevel		`G`	`F`	`L`	`D`	`D`	`Y`	`A`	`F`	`L`	`I`	`W`	`G`	`L`	`L`	`D`	`L`	`Y`	`E`	`A`	`T`	`G`	`D`	`x`	`E`	`Y`	`L`	`E`	`K`	`A`	`K`	`E`	`L`	`Q`	`D`	`I`	`Q`	`D`	`K`	`L`	`F`	`W`	`D`
			consensus		`A`			`E`						`A`		`A`			`A`					`S`	`L`			`A`	`W`			`W`			`K`			`E`	`T`		`I`
			sequence


.

H.sapiens	572	6.84e-39	`TVEHSNPPCW`		`G`	`F`	`L`	`E`	`D`	`Y`	`A`	`F`	`V`	`V`	`R`	`G`	`L`	`L`	`D`	`L`	`Y`	`E`	`A`	`S`	`Q`	`E`	`S`	`A`	`W`	`L`	`E`	`W`	`A`	`L`	`R`	`L`	`Q`	`D`	`T`	`Q`	`D`	`K`	`L`	`F`	`W`	`D`	`SQGGGYFCSE`
D.melanogaster	591	3.29e-38	`TLEKNASQID`		`G`	`F`	`L`	`D`	`D`	`Y`	`A`	`F`	`L`	`I`	`K`	`G`	`L`	`L`	`D`	`Y`	`Y`	`K`	`A`	`T`	`L`	`D`	`V`	`D`	`V`	`L`	`H`	`W`	`A`	`K`	`A`	`L`	`Q`	`D`	`T`	`Q`	`D`	`K`	`L`	`F`	`W`	`D`	`ERNGAYFFSQ`
A.aeolicus	481	1.95e-37	`RYMEGEAKYW`		`G`	`F`	`L`	`E`	`D`	`Y`	`A`	`Y`	`F`	`I`	`W`	`G`	`L`	`M`	`E`	`L`	`Y`	`E`	`A`	`T`	`L`	`D`	`S`	`K`	`Y`	`L`	`E`	`E`	`V`	`I`	`K`	`L`	`Q`	`E`	`I`	`Q`	`I`	`K`	`H`	`F`	`W`	`D`	`KENGGFFQTP`
B.subtilis	475	1.86e-34	`RYRDGEVKNK`		`G`	`F`	`I`	`D`	`D`	`Y`	`A`	`F`	`L`	`L`	`W`	`A`	`Y`	`L`	`D`	`L`	`Y`	`E`	`A`	`S`	`F`	`D`	`L`	`S`	`Y`	`L`	`Q`	`K`	`A`	`K`	`K`	`L`	`T`	`D`	`D`	`M`	`I`	`S`	`L`	`F`	`W`	`D`	`EEHGGFYFTG`
C.elegans	520	3.03e-32	`EVEQGNQEIR`		`A`	`F`	`S`	`D`	`D`	`Y`	`A`	`F`	`L`	`I`	`Q`	`A`	`L`	`L`	`D`	`L`	`Y`	`T`	`T`	`V`	`G`	`K`	`D`	`E`	`Y`	`L`	`K`	`K`	`A`	`V`	`E`	`L`	`Q`	`K`	`I`	`C`	`D`	`V`	`K`	`F`	`W`	`N`	`GNGYFISEKT`
A.thaliana	668	1.02e-29	`SYRQGPSKAP`		`A`	`F`	`L`	`D`	`D`	`Y`	`A`	`F`	`L`	`I`	`S`	`G`	`L`	`L`	`D`	`L`	`Y`	`E`	`N`	`G`	`G`	`G`	`I`	`E`	`W`	`L`	`K`	`W`	`A`	`I`	`K`	`L`	`Q`	`E`	`T`	`Q`	`A`	`K`	`D`	`H`	`D`	`G`	`AEPSGNSVSA`
M.thermoautotrophicum	472	1.97e-29	`RYRDGEAAIN`		`G`	`K`	`L`	`D`	`D`	`Y`	`A`	`F`	`L`	`I`	`W`	`G`	`L`	`L`	`E`	`M`	`Y`	`D`	`A`	`T`	`L`	`R`	`E`	`G`	`Y`	`I`	`R`	`K`	`A`	`L`	`E`	`L`	`T`	`E`	`I`	`L`	`R`	`D`	`N`	`F`	`R`	`D`	`SDGGFYLTDD`
A.fulgidus	460	5.52e-29	`RELLHTHNVE`		`G`	`L`	`S`	`E`	`D`	`Y`	`I`	`F`	`F`	`A`	`R`	`G`	`L`	`L`	`A`	`L`	`F`	`E`	`V`	`T`	`Q`	`R`	`H`	`E`	`Y`	`L`	`E`	`K`	`C`	`F`	`E`	`I`	`V`	`D`	`S`	`A`	`V`	`E`	`K`	`F`	`W`	`D`	`GEDGGFFDSE`
D.radiodaurans	487	4.44e-27	`TFKDGRASVE`		`G`	`L`	`L`	`E`	`D`	`H`	`A`	`L`	`Y`	`G`	`L`	`G`	`L`	`V`	`A`	`L`	`F`	`Q`	`A`	`G`	`G`	`D`	`L`	`A`	`H`	`L`	`H`	`W`	`A`	`R`	`E`	`L`	`W`	`N`	`I`	`V`	`R`	`R`	`D`	`F`	`W`	`D`	`EGAGVFYSSG`
M.tuberculosis	464	8.28e-25	`SLGGVVGDSA`		`A`	`I`	`L`	`E`	`D`	`H`	`A`	`M`	`L`	`A`	`T`	`G`	`L`	`L`	`A`	`L`	`Y`	`Q`	`L`	`T`	`S`	`E`	`G`	`A`	`W`	`L`	`T`	`A`	`A`	`T`	`G`	`L`	`L`	`D`	`T`	`A`	`V`	`A`	`H`	`F`	`G`	`D`	`PQRPGRWFDT`
A.pernix	469	3.66e-22	`VCYSGGECVE`		`G`	`M`	`L`	`P`	`D`	`Y`	`A`	`Y`	`T`	`A`	`A`	`A`	`L`	`A`	`S`	`L`	`Y`	`T`	`V`	`S`	`G`	`D`	`T`	`E`	`A`	`L`	`G`	`A`	`A`	`K`	`S`	`L`	`A`	`K`	`G`	`M`	`I`	`D`	`L`	`L`	`W`	`S`	`PGGGYFRLSP`

Motif 5 block diagrams

Name

Lowest
p-value

Motifs

H.sapiens

6.8e-39

D.melanogaster

3.3e-38

A.aeolicus

2e-37

B.subtilis

1.9e-34

C.elegans

3e-32

A.thaliana

1e-29

M.thermoautotrophicum

2e-29

A.fulgidus

5.5e-29

D.radiodaurans

4.4e-27

M.tuberculosis

8.3e-25

A.pernix

3.7e-22

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775	800	825	850

Motif 5 in BLOCKS format

BL   MOTIF 5 width=42 seqs=11
H.sapiens                (  572) GFLEDYAFVVRGLLDLYEASQESAWLEWALRLQDTQDKLFWD  1 
D.melanogaster           (  591) GFLDDYAFLIKGLLDYYKATLDVDVLHWAKALQDTQDKLFWD  1 
A.aeolicus               (  481) GFLEDYAYFIWGLMELYEATLDSKYLEEVIKLQEIQIKHFWD  1 
B.subtilis               (  475) GFIDDYAFLLWAYLDLYEASFDLSYLQKAKKLTDDMISLFWD  1 
C.elegans                (  520) AFSDDYAFLIQALLDLYTTVGKDEYLKKAVELQKICDVKFWN  1 
A.thaliana               (  668) AFLDDYAFLISGLLDLYENGGGIEWLKWAIKLQETQAKDHDG  1 
M.thermoautotrophicum    (  472) GKLDDYAFLIWGLLEMYDATLREGYIRKALELTEILRDNFRD  1 
A.fulgidus               (  460) GLSEDYIFFARGLLALFEVTQRHEYLEKCFEIVDSAVEKFWD  1 
D.radiodaurans           (  487) GLLEDHALYGLGLVALFQAGGDLAHLHWARELWNIVRRDFWD  1 
M.tuberculosis           (  464) AILEDHAMLATGLLALYQLTSEGAWLTAATGLLDTAVAHFGD  1 
A.pernix                 (  469) GMLPDYAYTAAALASLYTVSGDTEALGAAKSLAKGMIDLLWS  1 
//

Motif 5 position-specific scoring matrix

log-odds matrix: alength= 20 w= 42 n= 7545 bayes= 10.4473 E= 1.4e-090 
    90   -226   -349   -429   -483    340   -397   -419   -368   -519   -399   -231   -390   -359   -387   -202   -270   -365   -455   -466 
  -330   -186   -484   -472    385   -453   -386     59    -35     28    105   -358   -406   -358   -436   -318   -282   -170   -253   -138 
  -336   -225   -500   -442   -172   -466   -368     80   -368    285    -21   -357   -389   -276   -363     41   -260   -127   -337   -319 
  -272   -548    266    248   -588   -366   -322   -401   -189   -460   -372   -186     59    -78   -348   -273   -271   -365   -608   -492 
  -369   -324    387   -149   -436   -385   -293   -363   -379   -463   -387    -42   -457   -313   -409   -313   -347   -383   -438   -400 
  -479   -328   -523   -542    -35   -519    250   -347   -456   -369   -341   -346   -497   -370   -447   -408   -414   -390   -155    430 
   310    -57   -405   -386   -327   -201   -376     39   -337   -298   -218   -290   -410   -307   -363    -82   -174   -113   -384   -388 
  -373   -189   -464   -476    415   -470   -365   -177   -430   -102     11   -365   -401   -400   -466   -318   -364   -252   -211     75 
  -268   -167   -466   -411    131   -402   -308    -25   -334    249    -28   -299   -364   -255   -338   -285     39     41   -282     55 
   109   -125   -437   -397   -190    -16   -308    338   -315      0    -69   -265   -360   -265   -341   -239   -143    103   -297   -246 
    -6   -216   -138    -93   -278   -225   -113   -189     95    -51   -153    -35   -218    143    123     53     83   -191    321   -225 
    90   -226   -349   -429   -483    340   -397   -419   -368   -519   -399   -231   -390   -359   -387   -202   -270   -365   -455   -466 
  -386   -261   -527   -473   -158   -505   -360    -68   -399    302    -39   -383   -416   -299   -388   -395   -303   -171   -312     47 
  -122   -223   -490   -429   -167   -467   -359    -38   -357    289    115   -350   -377   -262   -350   -350   -258    -11   -332   -316 
   115   -401    275    140   -499   -312   -267   -379   -181   -440   -351    -97   -331    -94   -311     32   -234   -355   -526   -422 
  -363   -241   -508   -448   -165   -490   -372    -46   -376    295    125   -370   -393   -276   -366   -375   -280   -148   -334      7 
  -449   -306   -507   -516    209   -507   -168   -321   -438   -346   -315   -332   -477   -352   -429   -384   -392   -365   -139    428 
  -239   -435     73    243   -482   -336   -263   -345     68   -402   -308   -161   -308    225   -265   -222    163   -321   -509   -407 
   273    -39   -361   -333   -253   -193   -307   -119   -274    -91   -143     31   -371   -243   -307    -71     15     75   -320   -303 
  -188   -158   -398   -441   -403     81   -373   -256   -335   -409   -263   -184   -363   -278   -367    189    343     23   -440   -437 
  -165   -135   -246   -216     71    188   -197    -61   -141    108    -94   -121   -283    210   -206     44   -107    -91   -278   -207 
  -236   -337    272    119   -414     -5   -206   -317     68   -375   -281    -66   -303    -71    117   -174   -183   -308   -436   -344 
  -137   -181     31     21   -240     -7    121     83    -36     36   -122    -43   -220    -13   -117    120     84     35   -293   -211 
   116   -291     58    196   -354      1   -167   -265     79   -320   -222    -62   -256    -31   -169     47   -130   -256   -387   -292 
   -62   -147   -315   -308     98   -341    118   -161   -253   -220   -162   -204   -305   -222   -272   -196   -213     -7    290    360 
  -379   -254   -534   -474   -173   -512   -399     88   -402    301    -25   -396   -416   -300   -392   -401   -296   -146   -351   -341 
  -149   -231   -141    137   -295     -4    210   -212    159   -266   -167    -38   -224    144     56    -88     82   -210   -322   -234 
    69   -287   -218     24   -378   -303   -177   -268    256   -323   -233   -113   -308    -50    -71   -177   -165   -272    389   -306 
   303    155   -378   -357   -311   -175   -350   -207   -309   -295   -202   -268   -402   -282   -335    -54   -156     -9   -358   -369 
  -167    -86   -357   -307     77   -300   -231    205    184     73    -37   -193   -299   -179     23   -178     88     89   -241   -190 
    -7   -236   -133    174   -299     -4   -120   -216    201   -270   -171    -39   -226     -4     53     52    -87   -213   -328   -239 
  -379   -254   -534   -474   -173   -512   -399     88   -402    301    -25   -396   -416   -300   -392   -401   -296   -146   -351   -341 
   -19   -113   -299   -227   -177   -295   -168    -26   -176    -15    -61   -156   -286    353   -221   -165    151     64    166   -211 
  -283   -406    284    168   -499   -302   -258   -391    136   -454   -368    136   -342   -110   -314   -216   -241   -372   -523   -417 
  -210   -174     20   -264   -309     -9   -244    262   -202   -290   -187    -81   -322   -167   -270     62    307   -181   -370   -318 
    69    237   -373   -318   -148   -305   -234     10   -242      9    252   -203   -305    302   -271   -184    -98     89   -244   -196 
    -6   -122    165   -222   -187   -292   -212    248   -154   -146    -75   -152   -292   -129    118   -165   -105    148   -276   -219 
    -5   -222    111     33   -282   -219   -109   -202    229   -257   -157    -28   -212      5     48     54    -73     19   -315   -224 
  -208   -271    132   -142   -350   -231    226   -271    160    137   -234    156   -273    -58   -143   -117   -131   -272   -380   -283 
  -373   -187   -461   -474    424   -469    -58   -183   -429   -113   -195   -364   -399   -402   -467   -315   -366   -255   -210    -66 
  -423   -270   -253   -440   -139   -270   -366   -338   -369   -269   -278   -311   -435   -311   -233   -377   -351   -336    563   -172 
  -351   -312    377   -137   -425   -177   -270   -353   -348   -453   -376     43   -436   -286   -389   -138   -318   -372   -430   -384

Motif 5 position-specific probability matrix

letter-probability matrix: alength= 20 w= 42 n= 7545 E= 1.4e-090 
 0.172008  0.002689  0.005392  0.004075  0.001557  0.756574  0.001825  0.002151  0.004152  0.002792  0.001517  0.006337  0.003156  0.002632  0.004052  0.015127  0.006965  0.004739  0.000752  0.001507 
 0.009364  0.003549  0.002114  0.003023  0.642081  0.003092  0.001969  0.059125  0.041669  0.123746  0.050026  0.002627  0.002835  0.002656  0.002874  0.006809  0.006417  0.018294  0.003047  0.014683 
 0.008939  0.002723  0.001899  0.003739  0.013461  0.002821  0.002221  0.068200  0.004145  0.736096  0.020831  0.002649  0.003177  0.004707  0.004789  0.081619  0.007492  0.024602  0.001702  0.004190 
 0.013930  0.000290  0.382967  0.444502  0.000755  0.005661  0.003072  0.002427  0.014356  0.004196  0.001834  0.008637  0.071153  0.018475  0.005299  0.009277  0.006940  0.004710  0.000260  0.001262 
 0.007132  0.001363  0.888432  0.028371  0.002159  0.004951  0.003743  0.003163  0.003841  0.004111  0.001647  0.023440  0.001990  0.003637  0.003479  0.007044  0.004092  0.004175  0.000844  0.002388 
 0.003329  0.001333  0.001620  0.001865  0.034798  0.001962  0.160929  0.003544  0.002257  0.007881  0.002268  0.002859  0.001508  0.002447  0.002676  0.003650  0.002570  0.003969  0.006012  0.752520 
 0.788221  0.008703  0.003672  0.005497  0.004596  0.017743  0.002105  0.051257  0.005129  0.012907  0.005326  0.004203  0.002742  0.003793  0.004795  0.034856  0.013521  0.027115  0.001233  0.002589 
 0.006941  0.003473  0.002439  0.002950  0.789677  0.002743  0.002282  0.011485  0.002703  0.050258  0.025995  0.002503  0.002929  0.001988  0.002337  0.006793  0.003628  0.010365  0.004093  0.064419 
 0.014357  0.004049  0.002400  0.004609  0.110482  0.004407  0.003381  0.033024  0.005259  0.574471  0.019834  0.003954  0.003792  0.005413  0.005674  0.008543  0.059297  0.078708  0.002500  0.055846 
 0.196507  0.005427  0.002942  0.005095  0.011911  0.064121  0.003384  0.408786  0.005979  0.102327  0.014898  0.005014  0.003901  0.005071  0.005580  0.011743  0.016833  0.121276  0.002244  0.006958 
 0.088415  0.002881  0.023255  0.042025  0.006481  0.015035  0.013078  0.010586  0.102586  0.071746  0.008346  0.024673  0.010402  0.085508  0.138478  0.088706  0.080601  0.015817  0.163337  0.008045 
 0.172008  0.002689  0.005392  0.004075  0.001557  0.756574  0.001825  0.002151  0.004152  0.002792  0.001517  0.006337  0.003156  0.002632  0.004052  0.015127  0.006965  0.004739  0.000752  0.001507 
 0.006332  0.002115  0.001575  0.003011  0.014912  0.002164  0.002357  0.024422  0.003352  0.825827  0.018409  0.002203  0.002643  0.004012  0.004018  0.003980  0.005553  0.018142  0.002027  0.052944 
 0.039627  0.002744  0.002039  0.004077  0.013920  0.002801  0.002377  0.030180  0.004467  0.753832  0.053264  0.002783  0.003446  0.005153  0.005251  0.005423  0.007578  0.054989  0.001769  0.004279 
 0.204823  0.000800  0.407526  0.210299  0.001393  0.008240  0.004472  0.002841  0.015148  0.004826  0.002116  0.015990  0.004746  0.016519  0.006870  0.076866  0.008928  0.005082  0.000458  0.002057 
 0.007419  0.002421  0.001791  0.003588  0.014169  0.002400  0.002173  0.028453  0.003929  0.787185  0.057440  0.002420  0.003088  0.004677  0.004690  0.004589  0.006526  0.021200  0.001741  0.040099 
 0.004086  0.001552  0.001804  0.002225  0.188524  0.002132  0.008903  0.004228  0.002550  0.009253  0.002704  0.003141  0.001724  0.002763  0.003029  0.004304  0.002996  0.004731  0.006727  0.742626 
 0.017582  0.000634  0.100399  0.430757  0.001572  0.006958  0.004599  0.003581  0.085315  0.006296  0.002852  0.010261  0.005596  0.151492  0.009422  0.013216  0.140282  0.006393  0.000518  0.002275 
 0.609248  0.009841  0.004957  0.007961  0.007712  0.018715  0.003406  0.017233  0.007941  0.054190  0.008912  0.038802  0.003616  0.005904  0.007050  0.037506  0.050363  0.100045  0.001919  0.004679 
 0.025095  0.004310  0.003837  0.003748  0.002719  0.125409  0.002152  0.006672  0.005196  0.005977  0.003899  0.008793  0.003822  0.004626  0.004650  0.227681  0.489200  0.069529  0.000833  0.001853 
 0.029341  0.005079  0.011065  0.017908  0.072446  0.263385  0.007285  0.025655  0.020020  0.216377  0.012553  0.013586  0.006648  0.136078  0.014189  0.083523  0.021616  0.031602  0.002558  0.009086 
 0.017955  0.001249  0.398632  0.182624  0.002518  0.068981  0.006838  0.004348  0.084939  0.007608  0.003428  0.019882  0.005789  0.019441  0.133244  0.018371  0.012762  0.007000  0.000859  0.003530 
 0.035721  0.003688  0.075285  0.092612  0.008434  0.068263  0.065826  0.069629  0.041473  0.130529  0.010356  0.023269  0.010231  0.029048  0.026324  0.141251  0.081268  0.075624  0.002313  0.008857 
 0.206243  0.001711  0.090646  0.309879  0.003813  0.071979  0.008999  0.006259  0.091892  0.011089  0.005162  0.020493  0.007973  0.025581  0.018290  0.085222  0.018409  0.010087  0.001207  0.005064 
 0.059902  0.004650  0.006844  0.009459  0.087546  0.006711  0.064580  0.012861  0.009180  0.022231  0.007815  0.007650  0.005706  0.006824  0.008986  0.015875  0.010376  0.056541  0.131596  0.464667 
 0.006661  0.002215  0.001500  0.002991  0.013368  0.002054  0.001794  0.072380  0.003266  0.824640  0.020305  0.002022  0.002634  0.003975  0.003912  0.003829  0.005815  0.021501  0.001548  0.003590 
 0.032892  0.002597  0.022913  0.206539  0.005759  0.069335  0.122490  0.009019  0.160130  0.016178  0.007589  0.024107  0.009995  0.086317  0.087067  0.033533  0.080231  0.013878  0.001892  0.007538 
 0.148640  0.001769  0.013396  0.094228  0.003233  0.008782  0.008377  0.006103  0.313226  0.010842  0.004773  0.014394  0.005596  0.022468  0.036295  0.018108  0.014406  0.008997  0.261774  0.004592 
 0.751379  0.037881  0.004430  0.006705  0.005129  0.021228  0.002519  0.009344  0.006240  0.013181  0.005940  0.004915  0.002917  0.004498  0.005790  0.042287  0.015383  0.055792  0.001475  0.002967 
 0.029000  0.007091  0.005098  0.009515  0.075840  0.008962  0.005768  0.162863  0.190304  0.169053  0.018617  0.008262  0.005917  0.009176  0.069601  0.017918  0.083363  0.110114  0.003320  0.010218 
 0.087677  0.002518  0.024196  0.266965  0.005593  0.069622  0.012392  0.008773  0.213489  0.015687  0.007359  0.023924  0.009858  0.030891  0.085380  0.088173  0.024819  0.013561  0.001821  0.007302 
 0.006661  0.002215  0.001500  0.002991  0.013368  0.002054  0.001794  0.072380  0.003266  0.824640  0.020305  0.002022  0.002634  0.003975  0.003912  0.003829  0.005815  0.021501  0.001548  0.003590 
 0.080786  0.005899  0.007627  0.016500  0.013025  0.009230  0.008906  0.032731  0.015729  0.092234  0.015740  0.010671  0.006514  0.366505  0.012828  0.019559  0.128711  0.092224  0.055742  0.008839 
 0.012938  0.000772  0.434118  0.256337  0.001399  0.008783  0.004766  0.002615  0.135996  0.004390  0.001881  0.080606  0.004420  0.014868  0.006732  0.013782  0.008513  0.004489  0.000470  0.002126 
 0.021457  0.003864  0.069773  0.012772  0.005228  0.067108  0.005255  0.241146  0.013053  0.013705  0.006565  0.017924  0.005054  0.009991  0.009130  0.094670  0.380880  0.016862  0.001352  0.004211 
 0.148756  0.066924  0.004586  0.008799  0.015983  0.008652  0.005641  0.041957  0.009909  0.108314  0.138262  0.007691  0.005683  0.257054  0.009022  0.017183  0.022900  0.109585  0.003245  0.009855 
 0.088185  0.005540  0.190763  0.017080  0.012178  0.009419  0.006571  0.218312  0.018213  0.037055  0.014285  0.010942  0.006225  0.012991  0.134403  0.019597  0.021845  0.165387  0.002603  0.008406 
 0.088766  0.002764  0.131422  0.100021  0.006280  0.015616  0.013418  0.009661  0.259781  0.017180  0.008108  0.025836  0.010836  0.032887  0.082768  0.089331  0.027401  0.067864  0.001992  0.008068 
 0.021802  0.001969  0.151858  0.029918  0.003931  0.014445  0.136621  0.005999  0.161118  0.263511  0.004744  0.092493  0.007133  0.021193  0.021984  0.027338  0.018275  0.009026  0.001268  0.005373 
 0.006955  0.003540  0.002481  0.002977  0.836797  0.002776  0.019116  0.011046  0.002720  0.046689  0.006225  0.002517  0.002977  0.001955  0.002320  0.006916  0.003573  0.010161  0.004120  0.024142 
 0.004911  0.001982  0.010496  0.003772  0.017010  0.011027  0.002253  0.003757  0.004123  0.015838  0.003514  0.003646  0.002310  0.003693  0.011810  0.004503  0.003964  0.005770  0.874004  0.011617 
 0.008084  0.001481  0.828038  0.030864  0.002332  0.020889  0.004405  0.003391  0.004762  0.004412  0.001777  0.042230  0.002291  0.004366  0.003992  0.023642  0.004994  0.004494  0.0008
motif=6
starts: w=8, seq=0, l=865          
starts: w=8, seq=5, l=677          
starts: w=8, seq=10, l=681          
starts: w=11, seq=0, l=865          
starts: w=11, seq=5, l=677          
starts: w=11, seq=10, l=681          
starts: w=15, seq=0, l=865          
starts: w=15, seq=5, l=677          
starts: w=15, seq=10, l=681          
starts: w=21, seq=0, l=865          
starts: w=21, seq=5, l=677          
starts: w=21, seq=10, l=681          
starts: w=29, seq=0, l=865          
starts: w=29, seq=5, l=677          
starts: w=29, seq=10, l=681          
starts: w=41, seq=0, l=865          
starts: w=41, seq=5, l=677          
starts: w=41, seq=10, l=681          
starts: w=50, seq=0, l=865          
starts: w=50, seq=5, l=677          
starts: w=50, seq=10, l=681          

em: w=   8, psites=   2, iter=   0 
em: w=   8, psites=   2, iter=  10 
em: w=   8, psites=   2, iter=  20 
em: w=   8, psites=   2, iter=  30 
em: w=   8, psites=   2, iter=  40 
em: w=   8, psites=   4, iter=   0 
em: w=   8, psites=   4, iter=  10 
em: w=   8, psites=   4, iter=  20 
em: w=   8, psites=   4, iter=  30 
em: w=   8, psites=   4, iter=  40 
em: w=   8, psites=   8, iter=   0 
em: w=   8, psites=   8, iter=  10 
em: w=   8, psites=   8, iter=  20 
em: w=   8, psites=   8, iter=  30 
em: w=   8, psites=   8, iter=  40 
em: w=   8, psites=  12, iter=   0 
em: w=   8, psites=  12, iter=  10 
em: w=   8, psites=  12, iter=  20 
em: w=   8, psites=  12, iter=  30 
em: w=   8, psites=  12, iter=  40 
em: w=  11, psites=   2, iter=   0 
em: w=  11, psites=   2, iter=  10 
em: w=  11, psites=   2, iter=  20 
em: w=  11, psites=   2, iter=  30 
em: w=  11, psites=   2, iter=  40 
em: w=  11, psites=   4, iter=   0 
em: w=  11, psites=   8, iter=   0 
em: w=  11, psites=   8, iter=  10 
em: w=  11, psites=   8, iter=  20 
em: w=  11, psites=   8, iter=  30 
em: w=  11, psites=   8, iter=  40 
em: w=  11, psites=  12, iter=   0 
em: w=  11, psites=  12, iter=  10 
em: w=  11, psites=  12, iter=  20 
em: w=  15, psites=   2, iter=   0 
em: w=  15, psites=   2, iter=  10 
em: w=  15, psites=   2, iter=  20 
em: w=  15, psites=   2, iter=  30 
em: w=  15, psites=   2, iter=  40 
em: w=  15, psites=   4, iter=   0 
em: w=  15, psites=   8, iter=   0 
em: w=  15, psites=  12, iter=   0 
em: w=  15, psites=  12, iter=  10 
em: w=  15, psites=  12, iter=  20 
em: w=  15, psites=  12, iter=  30 
em: w=  15, psites=  12, iter=  40 
em: w=  21, psites=   2, iter=   0 
em: w=  21, psites=   4, iter=   0 
em: w=  21, psites=   8, iter=   0 
em: w=  21, psites=  12, iter=   0 
em: w=  29, psites=   2, iter=   0 
em: w=  29, psites=   4, iter=   0 
em: w=  29, psites=   8, iter=   0 
em: w=  29, psites=  12, iter=   0 
em: w=  41, psites=   2, iter=   0 
em: w=  41, psites=   4, iter=   0 
em: w=  41, psites=   8, iter=   0 
em: w=  41, psites=  12, iter=   0 
em: w=  50, psites=   2, iter=   0 
em: w=  50, psites=   4, iter=   0 
em: w=  50, psites=   8, iter=   0 
em: w=  50, psites=  12, iter=   0 93  0.002660






Time 132.33 secs.

P N
MOTIF 6 width = 27 sites = 11 llr = 560 E-value = 1.8e-075

NAME	START	P-VALUE				SITES
			Simplified	A	:	:	1	2	:	:	:	:	1	:	7	:	:	:	:	1	2	1	2	:	:	1	:	1	:	1	1
			pos.-specific	C	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:
			probability	D	:	a	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	2	:	:	:	:	:	1
			matrix	E	:	:	2	2	:	:	:	:	:	1	1	:	:	:	:	1	:	:	1	:	2	:	:	:	:	:	:
				F	4	:	:	:	3	:	:	a	:	:	:	:	:	a	:	:	:	:	:	:	:	5	:	2	:	1	:
				G	:	:	:	:	:	a	a	:	9	1	1	:	:	:	:	:	:	:	:	:	:	:	:	1	:	1	:
				H	:	:	:	1	2	:	:	:	:	:	:	:	:	:	1	1	1	4	:	:	1	:	:	:	1	3	2
				I	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	2	:	:	:	1	:	:	:
				K	:	:	:	1	:	:	:	:	:	:	:	:	a	:	:	1	:	1	:	:	:	:	:	:	:	:	:
				L	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	1	7	1	3	9	5	:	:	:
				M	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	2	:	:	1	:	2	:	1	1	:	:	:
				N	:	:	:	:	2	:	:	:	:	:	:	:	:	:	:	:	:	:	2	:	1	:	:	:	:	:	:
				P	:	:	:	:	:	:	:	:	:	:	:	8	:	:	9	1	5	1	:	:	:	:	:	:	:	:	1
				Q	1	:	1	1	:	:	:	:	:	1	1	1	:	:	:	:	:	:	:	:	1	:	:	:	:	1	:
				R	:	:	1	1	:	:	:	:	:	3	:	:	:	:	:	1	:	:	1	:	:	:	:	:	4	:	:
				S	:	:	2	:	:	:	:	:	:	5	:	:	:	:	:	:	1	1	:	:	1	:	:	:	1	:	1
				T	1	:	3	1	:	:	:	:	:	:	:	:	:	:	:	3	:	:	1	:	:	:	:	:	4	:	:
				V	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	1	2	:	1	:	:	:	:	:	:	:
				W	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1
				Y	5	:	1	:	3	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	1	4	4
.
			bits	6.3
				5.6
				5.0
				4.4
			Information	3.8
			content	3.1
			(73.5 bits)	2.5
				1.9
				1.3
				0.6
				0.0
.
			Multilevel		`Y`	`D`	`T`	`x`	`F`	`G`	`G`	`F`	`G`	`S`	`A`	`P`	`K`	`F`	`P`	`T`	`P`	`H`	`x`	`L`	`x`	`F`	`L`	`L`	`R`	`Y`	`Y`
			consensus		`F`				`Y`					`R`												`L`			`T`	`H`
			sequence


.

A.aeolicus	194	2.56e-29	`HRAFSELFSS`		`Y`	`D`	`E`	`H`	`F`	`G`	`G`	`F`	`G`	`S`	`A`	`P`	`K`	`F`	`P`	`T`	`P`	`H`	`N`	`L`	`M`	`F`	`L`	`G`	`R`	`Y`	`Y`	`YRYKREQALK`
B.subtilis	196	7.91e-26	`HRTFQQLASG`		`F`	`D`	`T`	`I`	`Y`	`G`	`G`	`F`	`G`	`Q`	`A`	`P`	`K`	`F`	`P`	`M`	`P`	`H`	`M`	`L`	`M`	`Y`	`L`	`L`	`R`	`Y`	`D`	`HNTGQENALY`
M.thermoautotrophicum	192	1.59e-24	`DMAYEYLRRN`		`F`	`D`	`R`	`K`	`N`	`G`	`G`	`F`	`G`	`S`	`Q`	`Q`	`K`	`F`	`P`	`T`	`P`	`H`	`N`	`I`	`H`	`F`	`L`	`L`	`T`	`Y`	`H`	`LRRGEGEALE`
D.radiodaurans	206	3.53e-23	`ARAVENAARL`		`Y`	`D`	`A`	`Q`	`F`	`G`	`G`	`F`	`G`	`R`	`A`	`P`	`K`	`F`	`P`	`A`	`P`	`S`	`T`	`L`	`D`	`F`	`L`	`L`	`T`	`Q`	`P`	`QGREMALHTL`
A.thaliana	347	4.22e-23	`GISREALSRS`		`Y`	`D`	`S`	`E`	`F`	`G`	`G`	`F`	`G`	`S`	`A`	`P`	`K`	`F`	`P`	`R`	`P`	`V`	`E`	`I`	`Q`	`L`	`M`	`L`	`Y`	`H`	`Y`	`KKLKESGKTS`
H.sapiens	255	1.21e-22	`NRCFQQLDEG`		`Y`	`D`	`E`	`E`	`Y`	`G`	`G`	`F`	`A`	`E`	`A`	`P`	`K`	`F`	`P`	`T`	`P`	`V`	`I`	`L`	`S`	`F`	`L`	`F`	`S`	`Y`	`W`	`LSHRLTQDGS`
C.elegans	206	3.33e-21	`KSIYSHKQSS`		`F`	`D`	`S`	`R`	`L`	`G`	`G`	`F`	`G`	`R`	`A`	`P`	`K`	`F`	`P`	`K`	`A`	`C`	`D`	`L`	`D`	`F`	`L`	`I`	`T`	`F`	`A`	`ASENESEKAK`
D.melanogaster	271	1.36e-20	`SEAINVHRQR`		`F`	`D`	`Q`	`T`	`H`	`G`	`G`	`F`	`G`	`S`	`E`	`P`	`K`	`F`	`P`	`E`	`V`	`P`	`R`	`L`	`N`	`F`	`L`	`F`	`H`	`G`	`Y`	`LVTKDPDVLD`
M.tuberculosis	194	1.37e-19	`DDAVAGVLRE`		`Q`	`D`	`T`	`A`	`H`	`G`	`G`	`F`	`G`	`G`	`A`	`P`	`K`	`F`	`P`	`P`	`S`	`A`	`L`	`L`	`E`	`A`	`L`	`M`	`R`	`H`	`Y`	`ERTRSPAALE`
A.fulgidus	191	4.65e-19	`DKGIEAVLDQ`		`T`	`D`	`Y`	`V`	`N`	`G`	`G`	`F`	`G`	`S`	`A`	`P`	`K`	`F`	`H`	`H`	`A`	`K`	`A`	`V`	`E`	`L`	`L`	`L`	`T`	`H`	`H`	`FFTGDEEVLK`
A.pernix	188	8.75e-19	`GKAVSSLEKV`		`Y`	`D`	`T`	`A`	`Y`	`G`	`G`	`F`	`G`	`R`	`G`	`M`	`K`	`F`	`P`	`M`	`H`	`H`	`A`	`L`	`L`	`L`	`L`	`A`	`R`	`A`	`S`	`MAGDRRALNM`

Motif 6 block diagrams

Name

Lowest
p-value

Motifs

A.aeolicus

2.6e-29

B.subtilis

7.9e-26

M.thermoautotrophicum

1.6e-24

D.radiodaurans

3.5e-23

A.thaliana

4.2e-23

H.sapiens

1.2e-22

C.elegans

3.3e-21

D.melanogaster

1.4e-20

M.tuberculosis

1.4e-19

A.fulgidus

4.6e-19

A.pernix

8.7e-19

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775	800	825	850

Motif 6 in BLOCKS format

BL   MOTIF 6 width=27 seqs=11
A.aeolicus               (  194) YDEHFGGFGSAPKFPTPHNLMFLGRYY  1 
B.subtilis               (  196) FDTIYGGFGQAPKFPMPHMLMYLLRYD  1 
M.thermoautotrophicum    (  192) FDRKNGGFGSQQKFPTPHNIHFLLTYH  1 
D.radiodaurans           (  206) YDAQFGGFGRAPKFPAPSTLDFLLTQP  1 
A.thaliana               (  347) YDSEFGGFGSAPKFPRPVEIQLMLYHY  1 
H.sapiens                (  255) YDEEYGGFAEAPKFPTPVILSFLFSYW  1 
C.elegans                (  206) FDSRLGGFGRAPKFPKACDLDFLITFA  1 
D.melanogaster           (  271) FDQTHGGFGSEPKFPEVPRLNFLFHGY  1 
M.tuberculosis           (  194) QDTAHGGFGGAPKFPPSALLEALMRHY  1 
A.fulgidus               (  191) TDYVNGGFGSAPKFHHAKAVELLLTHH  1 
A.pernix                 (  188) YDTAYGGFGRGMKFPMHHALLLLARAS  1 
//

Motif 6 position-specific scoring matrix

log-odds matrix: alength= 20 w= 27 n= 7725 bayes= 9.80938 E= 1.8e-075 
  -237   -155   -318   -313    252   -348    -28   -178   -259   -230   -174   -208   -310     61   -277   -201     18   -211   -103    362 
  -369   -324    387   -149   -436   -385   -293   -363   -379   -463   -387    -42   -457   -313   -409   -313   -347   -383   -438   -400 
    -5   -216   -126     91   -277   -217   -107   -197    -15   -253   -153    -25   -210    142     47    122    205   -194   -311     66 
    62   -215   -126     91   -275   -216    121     67     92   -250   -151    -25   -209    143     48    -72     83     20   -309   -219 
  -269   -181   -348   -343    235   -375    208   -203   -288    -59   -199    176   -338   -249   -303   -230   -252   -237   -111    325 
  -305   -339   -351   -439   -512    371   -406   -458   -372   -560   -441   -245   -441   -389   -396   -297   -381   -448   -462   -479 
  -305   -339   -351   -439   -512    371   -406   -458   -372   -560   -441   -245   -441   -389   -396   -297   -381   -448   -462   -479 
  -413   -228   -494   -515    435   -491   -414   -228   -468   -224   -241   -402   -432   -440   -502   -356   -405   -299   -254   -113 
  -103   -278   -292   -379   -462    362   -353   -397   -312   -508   -379   -183   -391   -332   -338   -229   -315   -383   -413   -427 
  -183   -257   -144     27   -334      3   -142   -249    -26   -302   -205    -40   -256    143    181    243   -111   -247   -356   -268 
   293    -42   -293    -84   -316    -52   -319   -218   -258   -299   -205   -221   -384     18   -308    -60   -156   -117   -361   -361 
  -194   -263   -321   -317   -376   -332   -302   -288   -246   -339     79   -256    405     55   -301   -191   -205   -287   -456   -421 
  -402   -320   -498   -474   -548   -475   -398   -358    411   -500   -397   -306   -447   -345    -80   -421   -355   -458   -455   -494 
  -413   -228   -494   -515    435   -491   -414   -228   -468   -224   -241   -402   -432   -440   -502   -356   -405   -299   -254   -113 
  -226   -290   -349   -350   -401   -357     87   -322   -279   -372   -341   -283    415   -238   -333   -223   -236   -320   -475   -437 
    -5   -217   -127     29   -277   -217    121   -196     93   -252    223    -26     43      7     48    -73    204   -194   -310   -220 
    21   -252   -320   -316   -374   -324     63   -283   -246   -338   -302   -251    379   -205   -301    -10   -200    -27   -452   -416 
    -5    219   -175   -132   -228   -240    310   -108     75   -200   -115    -63     47    -35   -137     47    -82    118   -290   -206 
    62   -205     34     27   -264   -218   -109     71    -19    -50    135    206   -211      2     46    -74     83   -176   -304   -217 
  -375   -249   -558   -503   -198   -529   -432    184   -433    279    -53   -417   -445   -335   -428   -422   -295     50   -380   -365 
  -134   -219    111     93   -279   -216    121   -199    -16    -54    223    133   -210    143   -100     54    -70   -196   -312   -221 
  -139   -196   -472   -480    403   -469   -338   -169   -427     16   -182   -359   -408   -387   -457   -322   -346   -240   -206     51 
  -376   -252   -526   -465   -169   -506   -391    -49   -394    302    137   -388   -408   -291   -383   -393   -293   -155   -345   -336 
   -53   -141   -444   -389    127    -48   -297    107   -310    233    147   -274   -343   -238   -319   -255   -161    -69   -280   -243 
  -202   -231   -198   -169   -300   -275    125   -215    -37   -294   -195    -72   -280    -56    214     52    275   -223   -338     77 
   -87   -117   -269   -262    160   -105    206   -142   -212   -197   -137   -162   -267     15   -232   -156   -181   -173    -92    354 
   -86   -115    -78   -251    131   -299    153   -140   -199   -195   -134   -159    -51   -174   -226    -39   -174   -170     98    356

Motif 6 position-specific probability matrix

letter-probability matrix: alength= 20 w= 27 n= 7725 E= 1.8e-075 
 0.017806  0.004416  0.006695  0.009138  0.255517  0.006414  0.023528  0.011425  0.008815  0.020750  0.007203  0.007443  0.005516  0.048374  0.008688  0.015261  0.051366  0.013785  0.008622  0.469238 
 0.007132  0.001363  0.888432  0.028371  0.002159  0.004951  0.003743  0.003163  0.003841  0.004111  0.001647  0.023440  0.001990  0.003637  0.003479  0.007044  0.004092  0.004175  0.000844  0.002388 
 0.088721  0.002884  0.025312  0.149754  0.006508  0.015889  0.013633  0.010035  0.047870  0.017651  0.008342  0.026333  0.011019  0.085223  0.081988  0.143383  0.187527  0.015422  0.002046  0.060459 
 0.141437  0.002903  0.025355  0.149972  0.006614  0.016011  0.066019  0.062497  0.100648  0.018003  0.008474  0.026417  0.011115  0.085645  0.082415  0.037495  0.080550  0.067972  0.002074  0.008386 
 0.014285  0.003684  0.005458  0.007385  0.225943  0.005321  0.120571  0.009605  0.007213  0.067850  0.006058  0.106509  0.004546  0.005643  0.007254  0.012465  0.007904  0.011508  0.008150  0.362648 
 0.011150  0.001229  0.005337  0.003796  0.001274  0.936810  0.001712  0.001643  0.004026  0.002105  0.001130  0.005748  0.002224  0.002138  0.003795  0.007883  0.003238  0.002662  0.000716  0.001385 
 0.011150  0.001229  0.005337  0.003796  0.001274  0.936810  0.001712  0.001643  0.004026  0.002105  0.001130  0.005748  0.002224  0.002138  0.003795  0.007883  0.003238  0.002662  0.000716  0.001385 
 0.005258  0.002657  0.001971  0.002253  0.903964  0.002384  0.001617  0.008082  0.002074  0.021639  0.004525  0.001935  0.002366  0.001507  0.001823  0.005204  0.002728  0.007489  0.003031  0.017490 
 0.044947  0.001875  0.008016  0.005781  0.001808  0.876042  0.002475  0.002497  0.006103  0.003013  0.001743  0.008815  0.003147  0.003190  0.005671  0.012619  0.005100  0.004170  0.001008  0.001982 
 0.025853  0.002171  0.022303  0.096564  0.004393  0.073101  0.010684  0.006983  0.044279  0
motif=7
starts: w=8, seq=0, l=865          
starts: w=8, seq=5, l=677          
starts: w=8, seq=10, l=681          
starts: w=11, seq=0, l=865          
starts: w=11, seq=5, l=677          
starts: w=11, seq=10, l=681          
starts: w=15, seq=0, l=865          
starts: w=15, seq=5, l=677          
starts: w=15, seq=10, l=681          
starts: w=21, seq=0, l=865          
starts: w=21, seq=5, l=677          
starts: w=21, seq=10, l=681          
starts: w=29, seq=0, l=865          
starts: w=29, seq=5, l=677          
starts: w=29, seq=10, l=681          
starts: w=41, seq=0, l=865          
starts: w=41, seq=5, l=677          
starts: w=41, seq=10, l=681          
starts: w=50, seq=0, l=865          
starts: w=50, seq=5, l=677          
starts: w=50, seq=10, l=681          

em: w=   8, psites=   2, iter=   0 
em: w=   8, psites=   2, iter=  10 
em: w=   8, psites=   2, iter=  20 
em: w=   8, psites=   2, iter=  30 
em: w=   8, psites=   2, iter=  40 
em: w=   8, psites=   4, iter=   0 
em: w=   8, psites=   4, iter=  10 
em: w=   8, psites=   4, iter=  20 
em: w=   8, psites=   4, iter=  30 
em: w=   8, psites=   4, iter=  40 
em: w=   8, psites=   8, iter=   0 
em: w=   8, psites=   8, iter=  10 
em: w=   8, psites=  12, iter=   0 
em: w=  11, psites=   2, iter=   0 
em: w=  11, psites=   4, iter=   0 
em: w=  11, psites=   4, iter=  10 
em: w=  11, psites=   4, iter=  20 
em: w=  11, psites=   4, iter=  30 
em: w=  11, psites=   4, iter=  40 
em: w=  11, psites=   8, iter=   0 
em: w=  11, psites=  12, iter=   0 
em: w=  15, psites=   2, iter=   0 
em: w=  15, psites=   2, iter=  10 
em: w=  15, psites=   2, iter=  20 
em: w=  15, psites=   2, iter=  30 
em: w=  15, psites=   2, iter=  40 
em: w=  15, psites=   4, iter=   0 
em: w=  15, psites=   4, iter=  10 
em: w=  15, psites=   4, iter=  20 
em: w=  15, psites=   4, iter=  30 
em: w=  15, psites=   4, iter=  40 
em: w=  15, psites=   8, iter=   0 
em: w=  15, psites=  12, iter=   0 
em: w=  15, psites=  12, iter=  10 
em: w=  15, psites=  12, iter=  20 
em: w=  15, psites=  12, iter=  30 
em: w=  15, psites=  12, iter=  40 
em: w=  21, psites=   2, iter=   0 
em: w=  21, psites=   4, iter=   0 
em: w=  21, psites=   4, iter=  10 
em: w=  21, psites=   8, iter=   0 
em: w=  21, psites=   8, iter=  10 
em: w=  21, psites=   8, iter=  20 
em: w=  21, psites=   8, iter=  30 
em: w=  21, psites=   8, iter=  40 
em: w=  21, psites=  12, iter=   0 
em: w=  29, psites=   2, iter=   0 
em: w=  29, psites=   4, iter=   0 
em: w=  29, psites=   4, iter=  10 
em: w=  29, psites=   4, iter=  20 
em: w=  29, psites=   4, iter=  30 
em: w=  29, psites=   4, iter=  40 
em: w=  29, psites=   8, iter=   0 
em: w=  29, psites=   8, iter=  10 
em: w=  29, psites=   8, iter=  20 
em: w=  29, psites=  12, iter=   0 
em: w=  41, psites=   2, iter=   0 
em: w=  41, psites=   2, iter=  10 
em: w=  41, psites=   2, iter=  20 
em: w=  41, psites=   2, iter=  30 
em: w=  41, psites=   2, iter=  40 
em: w=  41, psites=   4, iter=   0 
em: w=  41, psites=   8, iter=   0 
em: w=  41, psites=  12, iter=   0 
em: w=  50, psites=   2, iter=   0 
em: w=  50, psites=   4, iter=   0 
em: w=  50, psites=   8, iter=   0 
em: w=  50, psites=  12, iter=   0 .012558  0.005797  0.023779  0.008012  0.085558  0.208195  0.330681  0.020922  0.010723  0.001491  0.005953 
 0.703877  0.009628  0.007939  0.044446  0.004954  0.049825  0.003136  0.008632  0.008855  0.012815  0.005813  0.006805  0.003303  0.036035  0.007018  0.040655  0.015372  0.026325  0.001443  0.003123 
 0.024080  0.002088  0.006579  0.008867  0.003288  0.007161  0.003508  0.005319  0.009655  0.009748  0.041699  0.005311  0.780698  0.046441  0.007349  0.016335  0.010937  0.008116  0.000747  0.002072 
 0.005687  0.001405  0.001921  0.002977  0.000998  0.002660  0.001815  0.003270  0.920150  0.003196  0.001539  0.003766  0.002124  0.002915  0.033907  0.003337  0.003856  0.002481  0.000753  0.001245 
 0.005258  0.002657  0.001971  0.002253  0.903964  0.002384  0.001617  0.008082  0.002074  0.021639  0.004525  0.001935  0.002366  0.001507  0.001823  0.005204  0.002728  0.007489  0.003031  0.017490 
 0.019288  0.001726  0.005414  0.007073  0.002764  0.006004  0.052292  0.004217  0.007688  0.007768  0.002268  0.004404  0.836165  0.006094  0.005904  0.013162  0.008797  0.006468  0.000653  0.001853 
 0.088996  0.002872  0.025149  0.097592  0.006526  0.015890  0.066129  0.010099  0.101066  0.017796  0.113230  0.026247  0.063552  0.033248  0.082811  0.037236  0.185698  0.015496  0.002057  0.008311 
 0.106259  0.002256  0.006595  0.008939  0.003334  0.007565  0.044165  0.005520  0.009654  0.009798  0.002977  0.005507  0.651531  0.007655  0.007329  0.057568  0.011310  0.049128  0.000767  0.002142 
 0.088810  0.059013  0.018067  0.031977  0.009137  0.013552  0.244773  0.018569  0.089532  0.025424  0.010815  0.020258  0.065300  0.024921  0.022892  0.085332  0.025597  0.134526  0.002363  0.009142 
 0.141841  0.003124  0.077000  0.096435  0.007124  0.015755  0.013437  0.064333  0.046462  0.072024  0.061473  0.130613  0.010921  0.032295  0.081521  0.036766  0.080734  0.017479  0.002143  0.008520 
 0.006839  0.002301  0.001272  0.002442  0.011230  0.001822  0.001425  0.140019  0.002649  0.706030  0.016674  0.001742  0.002155  0.003107  0.003049  0.003312  0.005868  0.083762  0.001261  0.003041 
 0.036501  0.002824  0.131244  0.151802  0.006440  0.015950  0.066239  0.009865  0.047626  0.069964  0.113204  0.078947  0.011030  0.085697  0.029554  0.089668  0.027944  0.015228  0.002028  0.008244 
 0.035057  0.003321  0.002302  0.002866  0.724338  0.002770  0.002747  0.012135  0.002745  0.114250  0.006808  0.002604  0.002794  0.002179  0.002486  0.006587  0.004108  0.011218  0.004214  0.054471 
 0.006786  0.002243  0.001583  0.003173  0.013775  0.002148  0.001901  0.027970  0.003469  0.825922  0.062138  0.002129  0.002781  0.004220  0.004169  0.004037  0.005944  0.020271  0.001613  0.003728 
 0.063796  0.004859  0.002791  0.005388  0.107524  0.051424  0.003653  0.082587  0.006178  0.511477  0.066919  0.004697  0.004365  0.006122  0.006508  0.010517  0.014818  0.036742  0.002532  0.007102 
 0.022668  0.002605  0.015368  0.024801  0.005555  0.010651  0.067731  0.008840  0.041111  0.013334  0.006243  0.019094  0.006773  0.021601  0.261515  0.088545  0.303897  0.012655  0.001689  0.065322 
 0.050364  0.005746  0.009399  0.012949  0.134376  0.034497  0.119091  0.014642  0.012253  0.025973  0.009317  0.010203  0.007415  0.035169  0.011872  0.020840  0.012934  0.017931  0.009327  0.445702 
 0.050854  0.005825  0.035319  0.014043  0.109956  0.008984  0.082608  0.014875  0.013404  0.026362  0.009490  0.010445  0.033051  0.009512  0.012359  0.047089  0.013531  0.018272  0.034701  0.449321






Time 155.56 secs.

P N
MOTIF 7 width = 28 sites = 8 llr = 436 E-value = 3.5e-038

NAME	START	P-VALUE				SITES
			Simplified	A	:	:	:	:	:	:	:	:	:	:	:	9	:	:	:	3	1	:	:	4	6	:	1	:	:	1	1	1
			pos.-specific	C	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:
			probability	D	:	:	:	:	:	:	3	4	:	a	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
			matrix	E	:	:	:	:	1	:	6	:	:	:	:	:	4	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:
				F	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				G	:	1	:	:	:	:	:	:	:	:	9	:	:	:	:	6	:	1	:	:	:	:	:	:	:	:	:	5
				H	:	:	:	:	:	:	:	:	3	:	:	:	:	:	:	:	:	:	:	:	:	3	:	:	:	:	:	1
				I	1	4	1	:	:	1	:	:	:	:	:	:	3	:	:	:	:	:	1	1	:	:	:	:	1	:	:	:
				K	:	:	:	:	1	8	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				L	5	:	3	:	4	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	1	a	8	1	9	:
				M	:	1	:	:	1	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:
				N	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	8	:	:	:	:	1	6	:	:	:	:	:
				P	:	3	:	:	3	:	:	1	:	:	:	1	:	9	:	:	:	:	:	:	1	:	:	:	:	:	:	:
				Q	:	:	:	:	:	:	:	:	3	:	:	:	:	1	:	:	:	:	:	1	:	3	1	:	:	:	:	:
				R	:	:	:	a	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	6	:	:
				S	:	1	:	:	:	1	:	1	:	:	1	:	:	:	8	:	:	9	3	4	1	:	:	:	:	:	:	1
				T	:	:	:	:	:	:	:	:	:	:	:	:	3	:	1	:	1	:	:	:	:	:	:	:	:	1	:	:
				V	4	:	6	:	:	:	:	3	:	:	:	:	1	:	:	1	:	:	6	:	:	1	:	:	1	:	:	:
				W	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				Y	:	:	:	:	:	:	:	:	3	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:	:	:	:	1
.
			bits	6.3
				5.6
				5.0
				4.4
			Information	3.8
			content	3.1
			(78.7 bits)	2.5
				1.9
				1.3
				0.6
				0.0
.
			Multilevel		`L`	`I`	`V`	`R`	`L`	`K`	`E`	`D`	`H`	`D`	`G`	`A`	`E`	`P`	`S`	`G`	`N`	`S`	`V`	`A`	`A`	`H`	`N`	`L`	`L`	`R`	`L`	`G`
			consensus		`V`	`P`	`L`		`P`		`D`	`V`	`Q`				`I`			`A`			`S`	`S`		`Q`
			sequence										`Y`				`T`


.

M.thermoautotrophicum	526	6.09e-29	`GGFYLTDDPD`		`V`	`I`	`V`	`R`	`P`	`K`	`E`	`S`	`M`	`D`	`G`	`A`	`I`	`P`	`S`	`G`	`N`	`S`	`V`	`Q`	`M`	`Q`	`N`	`L`	`L`	`R`	`L`	`G`	`GLLEDEGLID`
A.aeolicus	538	1.82e-28	`FFQTPDFFTE`		`I`	`P`	`V`	`R`	`K`	`K`	`E`	`V`	`Y`	`D`	`G`	`A`	`I`	`P`	`S`	`G`	`N`	`S`	`V`	`S`	`A`	`Y`	`N`	`L`	`I`	`R`	`L`	`G`	`RLISRSEYEK`
B.subtilis	532	1.36e-26	`FYFTGHDAEA`		`L`	`I`	`V`	`R`	`E`	`K`	`E`	`V`	`Y`	`D`	`G`	`A`	`V`	`P`	`S`	`G`	`N`	`S`	`V`	`A`	`A`	`V`	`Q`	`L`	`L`	`R`	`L`	`G`	`QVTGDLSLIE`
H.sapiens	630	1.36e-26	`FCSEAELGAG`		`L`	`P`	`L`	`R`	`L`	`K`	`D`	`D`	`Q`	`D`	`G`	`A`	`E`	`P`	`S`	`A`	`N`	`S`	`V`	`S`	`A`	`H`	`N`	`L`	`L`	`R`	`L`	`H`	`GFTGHKDWMD`
D.melanogaster	648	2.05e-26	`YFFSQQDAPN`		`V`	`I`	`V`	`R`	`L`	`K`	`E`	`D`	`H`	`D`	`G`	`A`	`E`	`P`	`C`	`G`	`N`	`S`	`V`	`S`	`A`	`H`	`N`	`L`	`V`	`L`	`L`	`A`	`HYYDENAYLQ`
C.elegans	575	7.90e-21	`YFISEKTDED`		`V`	`S`	`V`	`R`	`M`	`I`	`E`	`D`	`Q`	`D`	`G`	`A`	`E`	`P`	`T`	`A`	`T`	`S`	`I`	`A`	`S`	`N`	`N`	`L`	`L`	`R`	`L`	`Y`	`DILEKEEYRE`
M.tuberculosis	522	3.05e-17	`WFDTADDAER`		`L`	`M`	`L`	`R`	`P`	`S`	`D`	`P`	`L`	`D`	`G`	`A`	`T`	`P`	`S`	`G`	`A`	`S`	`S`	`I`	`A`	`E`	`A`	`L`	`L`	`T`	`A`	`G`	`HVVDGARAER`
A.fulgidus	515	1.18e-16	`GGFFDSERAV`		`L`	`G`	`I`	`R`	`L`	`K`	`N`	`F`	`H`	`D`	`S`	`P`	`T`	`Q`	`S`	`V`	`N`	`G`	`S`	`A`	`P`	`Q`	`L`	`L`	`L`	`A`	`L`	`S`	`AITGERRYEE`

Motif 7 block diagrams

Name

Lowest
p-value

Motifs

M.thermoautotrophicum

6.1e-29

A.aeolicus

1.8e-28

B.subtilis

1.4e-26

H.sapiens

1.4e-26

D.melanogaster

2.1e-26

C.elegans

7.9e-21

M.tuberculosis

3e-17

A.fulgidus

1.2e-16

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775

Motif 7 in BLOCKS format

BL   MOTIF 7 width=28 seqs=8
M.thermoautotrophicum    (  526) VIVRPKESMDGAIPSGNSVQMQNLLRLG  1 
A.aeolicus               (  538) IPVRKKEVYDGAIPSGNSVSAYNLIRLG  1 
B.subtilis               (  532) LIVREKEVYDGAVPSGNSVAAVQLLRLG  1 
H.sapiens                (  630) LPLRLKDDQDGAEPSANSVSAHNLLRLH  1 
D.melanogaster           (  648) VIVRLKEDHDGAEPCGNSVSAHNLVLLA  1 
C.elegans                (  575) VSVRMIEDQDGAEPTATSIASNNLLRLY  1 
M.tuberculosis           (  522) LMLRPSDPLDGATPSGASSIAEALLTAG  1 
A.fulgidus               (  515) LGIRLKNFHDSPTQSVNGSAPQLLLALS  1 
//

Motif 7 position-specific scoring matrix

log-odds matrix: alength= 20 w= 28 n= 7713 bayes= 10.6491 E= 3.5e-038 
  -328   -202   -578   -544   -220   -522   -480    192   -474    214    -92   -426   -485   -403   -497   -424   -253    250   -413   -375 
  -136    -80   -300   -259   -150     22   -209    278   -184   -109    190   -157    199   -143   -230     63    -78    -21   -242   -190 
  -259   -172   -508   -492   -262   -488   -444    188   -437     96   -137   -393   -444   -401   -456   -392   -211    330   -445   -402 
  -437   -293   -494   -514   -511   -445   -289   -415   -174   -473   -429   -323   -409   -254    398   -399   -389   -500   -397   -465 
  -151   -167   -170     29   -211   -248   -144    -86     90    154    163    -74    178    -34   -121   -110    -87   -119   -287   -219 
  -348   -291   -426   -382   -491   -425   -326    -81    400   -434   -337   -247   -408   -240    -53   -139   -295   -383   -423   -435 
  -269   -449    161    295   -532   -304   -269   -391   -181   -455   -369    150   -327    -82   -326   -221   -240   -366   -558   -440 
  -133   -131    205   -128     85   -224   -139    -65    -75   -168    -89    -47     88    -47   -150     71    -70    153   -269   -186 
  -224   -156   -252   -242    -35   -310    349   -132   -177    -45    130    -74   -288    205   -179   -168   -152   -161   -179    229 
  -370   -324    387   -152   -437   -382   -294   -366   -377   -464   -389    -45   -452   -312   -409   -312   -346   -385   -438   -400 
  -222   -265   -278   -366   -450    359   -340   -386   -300   -496   -368   -169   -378   -318   -327    -47   -301   -371   -402   -415 
   309    -79   -417   -409   -377   -203   -394   -285   -369   -369   -274   -287     77   -317   -386    -93   -171   -183   -418   -424 
  -189   -121   -277    174   -196   -322   -253    245   -205   -140    -81   -190   -317   -162   -267   -191    207    126   -301   -242 
  -183   -251   -307   -304   -366   -319   -291   -280   -235   -330   -299   -243    408     83   -290   -180   -194   -277   -444   -408 
  -182    124   -330   -399   -339   -302   -319   -288   -265   -376   -262    -99   -298   -264   -289    352    159   -332   -380   -335 
    75   -178   -333   -402   -437    327   -371   -338   -342   -454   -345   -211   -355   -325   -361   -161   -221     21   -427   -432 
  -130   -235   -205   -377   -379   -303   -123   -270   -271   -419   -321    468   -355   -210   -339   -139    -25   -334   -366   -358 
  -156   -137   -338   -422   -406     27   -357   -355   -332   -438   -331   -151   -329   -302   -358    363     20   -328   -443   -404 
  -178   -124   -420   -403   -263   -393   -346    161   -349   -186   -148   -310   -361   -318   -360    103   -147    339   -396   -358 
   209    -84   -247   -209   -267   -199   -218    103   -144   -241   -155   -133   -281    132   -210    199    -90   -124   -326   -277 
   286    -30   -356   -333   -303   -170   -326   -201   -281   -286     98   -241     -2   -251   -315     46   -139   -109   -351   -352 
  -172   -197   -149      2   -224   -243    353   -213    -62   -254   -157    127   -231    223   -109    -98    -97      1   -268     77 
  -110   -232   -185   -255   -334   -292   -112   -223   -164   -140   -250    451   -316     39   -237   -128   -162   -272   -341   -309 
  -401   -277   -536   -496   -201   -499   -412    -81   -422    313    -57   -411   -428   -324   -412   -417   -322   -184   -369   -355 
  -341   -218   -512   -456   -168   -486   -385    125   -385    283    -19   -372   -401   -289   -379   -375   -260     58   -343   -327 
    -6   -173   -277   -224   -287   -283   -178   -148    -32    -29   -165   -136   -290    -80    320   -164     85   -174   -313   -276 
   -70   -215   -487   -431   -165   -436   -362    -36   -359    296    -12   -348   -376   -265   -353   -327   -253   -129   -331   -315 
   -50   -236   -222   -268   -360    322     69   -301   -204   -393   -288   -109   -329   -196   -261     -3   -215   -298   -373     27

Motif 7 position-specific probability matrix

letter-probability matrix: alength= 20 w= 28 n= 7713 E= 3.5e-038 
 0.009493  0.003177  0.001108  0.001843  0.009639  0.001917  0.001026  0.148047  0.001982  0.450538  0.012767  0.001643  0.001639  0.001939  0.001888  0.003250  0.007841  0.336415  0.001008  0.002838 
 0.035933  0.007414  0.007584  0.013271  0.015737  0.083267  0.006710  0.270004  0.014828  0.047771  0.089705  0.010575  0.187139  0.011753  0.012016  0.094992  0.026356  0.051400  0.003292  0.010254 
 0.015282  0.003926  0.001793  0.002640  0.007235  0.002428  0.001315  0.144447  0.002567  0.198588  0.009338  0.002066  0.002177  0.001978  0.002503  0.004060  0.010519  0.583971  0.000804  0.002361 
 0.004442  0.001697  0.001971  0.002265  0.001285  0.003271  0.003842  0.002209  0.015877  0.003841  0.001230  0.003347  0.002774  0.005452  0.935037  0.003887  0.003062  0.001860  0.001128  0.001523 
 0.032380  0.004060  0.018623  0.097599  0.010317  0.012857  0.010548  0.021662  0.099436  0.295800  0.074642  0.018818  0.162251  0.025170  0.025537  0.028681  0.024743  0.026069  0.002416  0.008392 
 0.008250  0.001714  0.003164  0.005636  0.001475  0.003763  0.002985  0.022409  0.851435  0.005037  0.002323  0.005686  0.002788  0.006035  0.040882  0.023544  0.005876  0.004179  0.000940  0.001879 
 0.014267  0.000574  0.185219  0.615138  0.001112  0.008711  0.004424  0.002614  0.015102  0.004355  0.001870  0.088704  0.004879  0.018041  0.006180  0.013336  0.008587  0.004704  0.000369  0.001813 
 0.036628  0.005211  0.250668  0.032802  0.080287  0.015169  0.010861  0.025047  0.031695  0.031792  0.013034  0.022710  0.086611  0.022962  0.020964  0.100738  0.027951  0.171564  0.002738  0.010567 
 0.019521  0.004375  0.010561  0.014884  0.034873  0.008317  0.321777  0.015669  0.015563  0.074922  0.059178  0.018798  0.006386  0.131831  0.017171  0.019181  0.015746  0.019462  0.005082  0.186701 
 0.007101  0.001366  0.889213  0.027866  0.002153  0.005074  0.003726  0.003111  0.003881  0.
motif=8
starts: w=8, seq=0, l=865          
starts: w=8, seq=5, l=677          
starts: w=8, seq=10, l=681          
starts: w=11, seq=0, l=865          
starts: w=11, seq=5, l=677          
starts: w=11, seq=10, l=681          
starts: w=15, seq=0, l=865          
starts: w=15, seq=5, l=677          
starts: w=15, seq=10, l=681          
starts: w=21, seq=0, l=865          
starts: w=21, seq=5, l=677          
starts: w=21, seq=10, l=681          
starts: w=29, seq=0, l=865          
starts: w=29, seq=5, l=677          
starts: w=29, seq=10, l=681          
starts: w=41, seq=0, l=865          
starts: w=41, seq=5, l=677          
starts: w=41, seq=10, l=681          
starts: w=50, seq=0, l=865          
starts: w=50, seq=5, l=677          
starts: w=50, seq=10, l=681          

em: w=   8, psites=   2, iter=   0 
em: w=   8, psites=   2, iter=  10 
em: w=   8, psites=   2, iter=  20 
em: w=   8, psites=   2, iter=  30 
em: w=   8, psites=   2, iter=  40 
em: w=   8, psites=   4, iter=   0 
em: w=   8, psites=   4, iter=  10 
em: w=   8, psites=   4, iter=  20 
em: w=   8, psites=   4, iter=  30 
em: w=   8, psites=   4, iter=  40 
em: w=   8, psites=   8, iter=   0 
em: w=   8, psites=   8, iter=  10 
em: w=   8, psites=  12, iter=   0 
em: w=  11, psites=   2, iter=   0 
em: w=  11, psites=   4, iter=   0 
em: w=  11, psites=   4, iter=  10 
em: w=  11, psites=   4, iter=  20 
em: w=  11, psites=   4, iter=  30 
em: w=  11, psites=   4, iter=  40 
em: w=  11, psites=   8, iter=   0 
em: w=  11, psites=  12, iter=   0 
em: w=  15, psites=   2, iter=   0 
em: w=  15, psites=   2, iter=  10 
em: w=  15, psites=   2, iter=  20 
em: w=  15, psites=   2, iter=  30 
em: w=  15, psites=   2, iter=  40 
em: w=  15, psites=   4, iter=   0 
em: w=  15, psites=   4, iter=  10 
em: w=  15, psites=   4, iter=  20 
em: w=  15, psites=   4, iter=  30 
em: w=  15, psites=   4, iter=  40 
em: w=  15, psites=   8, iter=   0 
em: w=  15, psites=  12, iter=   0 
em: w=  15, psites=  12, iter=  10 
em: w=  15, psites=  12, iter=  20 
em: w=  15, psites=  12, iter=  30 
em: w=  15, psites=  12, iter=  40 
em: w=  21, psites=   2, iter=   0 
em: w=  21, psites=   4, iter=   0 
em: w=  21, psites=   8, iter=   0 
em: w=  21, psites=   8, iter=  10 
em: w=  21, psites=   8, iter=  20 
em: w=  21, psites=   8, iter=  30 
em: w=  21, psites=   8, iter=  40 
em: w=  21, psites=  12, iter=   0 
em: w=  29, psites=   2, iter=   0 
em: w=  29, psites=   4, iter=   0 
em: w=  29, psites=   4, iter=  10 
em: w=  29, psites=   8, iter=   0 
em: w=  29, psites=   8, iter=  10 
em: w=  29, psites=   8, iter=  20 
em: w=  29, psites=  12, iter=   0 
em: w=  41, psites=   2, iter=   0 
em: w=  41, psites=   2, iter=  10 
em: w=  41, psites=   2, iter=  20 
em: w=  41, psites=   2, iter=  30 
em: w=  41, psites=   2, iter=  40 
em: w=  41, psites=   4, iter=   0 
em: w=  41, psites=   4, iter=  10 
em: w=  41, psites=   4, iter=  20 
em: w=  41, psites=   4, iter=  30 
em: w=  41, psites=   4, iter=  40 
em: w=  41, psites=   8, iter=   0 
em: w=  41, psites=  12, iter=   0 
em: w=  50, psites=   2, iter=   0 
em: w=  50, psites=   4, iter=   0 
em: w=  50, psites=   8, iter=   0 
em: w=  50, psites=  12, iter=   0 004084  0.001621  0.023053  0.002051  0.003663  0.003488  0.007084  0.004116  0.004117  0.000847  0.002383 
 0.019833  0.002056  0.008815  0.006310  0.001962  0.863232  0.002709  0.002697  0.006630  0.003270  0.001884  0.009738  0.003430  0.003495  0.006131  0.044399  0.005638  0.004534  0.001085  0.002153 
 0.782556  0.007449  0.003367  0.004695  0.003261  0.017447  0.001862  0.005430  0.004122  0.007910  0.003597  0.004301  0.080435  0.003537  0.004084  0.032361  0.013858  0.016730  0.000972  0.002029 
 0.024914  0.005569  0.008883  0.266455  0.011410  0.007680  0.004940  0.213692  0.012829  0.038552  0.013750  0.008401  0.005243  0.010308  0.009329  0.016343  0.190289  0.142084  0.002195  0.007133 
 0.025916  0.002267  0.007216  0.009695  0.003527  0.007841  0.003802  0.005646  0.010439  0.010344  0.003040  0.005843  0.798691  0.056636  0.007947  0.017635  0.011777  0.008670  0.000815  0.002256 
 0.026090  0.030436  0.006169  0.005021  0.004239  0.008800  0.003136  0.005325  0.008490  0.007555  0.003906  0.015792  0.005997  0.005095  0.007992  0.708423  0.136586  0.005928  0.001265  0.003754 
 0.155151  0.003767  0.006024  0.004903  0.002155  0.689619  0.002180  0.003773  0.004948  0.004401  0.002203  0.007287  0.004038  0.003348  0.004841  0.020205  0.009785  0.068549  0.000913  0.001908 
 0.037454  0.002533  0.014650  0.005834  0.003209  0.008750  0.012212  0.006044  0.008100  0.005608  0.002603  0.803724  0.004036  0.007406  0.005664  0.023532  0.038175  0.005870  0.001393  0.003203 
 0.031241  0.004978  0.005845  0.004273  0.002662  0.085931  0.002398  0.003338  0.005315  0.004901  0.002434  0.011004  0.004812  0.003923  0.004939  0.760561  0.052175  0.006122  0.000820  0.002329 
 0.026873  0.005463  0.003295  0.004886  0.007173  0.004681  0.002590  0.119552  0.004740  0.028145  0.008646  0.003655  0.003872  0.003495  0.004876  0.125845  0.016391  0.621499  0.001133  0.003191 
 0.390817  0.007232  0.010956  0.018804  0.007006  0.017972  0.006279  0.080048  0.019513  0.019212  0.008237  0.012519  0.006716  0.079483  0.013766  0.244582  0.024262  0.025148  0.001845  0.005605 
 0.667778  0.010449  0.005159  0.007959  0.005448  0.022017  0.002975  0.009761  0.007551  0.014008  0.047520  0.005923  0.046449  0.005596  0.006675  0.084664  0.017245  0.027944  0.001547  0.003330 
 0.027992  0.003296  0.021595  0.081088  0.009392  0.013241  0.329459  0.008965  0.034568  0.017514  0.008113  0.075985  0.009516  0.149397  0.027858  0.031113  0.023058  0.059778  0.002754  0.065317 
 0.043025  0.002582  0.016873  0.013640  0.004376  0.009440  0.013107  0.008389  0.017087  0.038790  0.004267  0.714852  0.005267  0.041722  0.011416  0.025287  0.014691  0.009035  0.001658  0.004498 
 0.005699  0.001894  0.001479  0.002568  0.011029  0.002253  0.001639  0.022342  0.002846  0.891484  0.016272  0.001824  0.002431  0.003362  0.003412  0.003424  0.004854  0.016548  0.001366  0.003273 
 0.008663  0.002852  0.001741  0.003391  0.013876  0.002461  0.001977  0.093182  0.003696  0.726630  0.021138  0.002387  0.002936  0.004285  0.004276  0.004586  0.007475  0.088859  0.001631  0.003958 
 0.088565  0.003899  0.008914  0.016947  0.006060  0.010035  0.008302  0.014021  0.042443  0.083472  0.007646  0.012274  0.006337  0.018312  0.545826  0.019752  0.081731  0.017810  0.002016  0.005639 
 0.056691  0.002907  0.002079  0.004023  0.014193  0.003470  0.002323  0.030532  0.004415  0.796159  0.022151  0.002823  0.003493  0.005045  0.005137  0.006399  0.007840  0.024242  0.001775  0.004302 
 0.065181  0.002509  0.013063  0.012483  0.003657  0.666654  0.046030  0.004869  0.012945  0.006696  0.003267  0.014772  0.004811  0.008193  0.009677  0.060146  0.010210  0.007535  0.001331  0.045971






Time 181.99 secs.

P N
MOTIF 8 width = 23 sites = 10 llr = 412 E-value = 3.8e-038

NAME	START	P-VALUE				SITES
			Simplified	A	:	1	1	3	4	:	:	:	:	:	:	4	:	:	:	:	1	:	1	1	2	:	2
			pos.-specific	C	:	:	1	:	:	:	:	a	:	:	:	:	a	:	:	:	:	:	:	:	1	:	:
			probability	D	2	:	1	:	:	:	:	:	1	:	:	:	:	2	:	:	:	:	6	:	2	:	:
			matrix	E	1	:	:	:	:	:	:	:	2	1	:	:	:	1	1	:	:	1	:	1	2	5	:
				F	:	:	:	:	1	:	:	:	:	:	3	:	:	:	:	:	:	1	:	:	:	:	:
				G	6	2	1	:	:	:	:	:	:	4	1	:	:	:	:	:	:	:	:	:	:	:	:
				H	:	:	:	:	:	:	:	:	2	1	1	:	:	1	:	:	:	:	:	:	:	:	:
				I	:	:	:	:	:	:	3	:	:	:	:	:	:	:	:	:	1	1	:	2	:	:	:
				K	:	5	:	:	:	:	:	:	1	:	:	1	:	1	:	:	:	1	:	:	:	1	:
				L	:	:	:	:	:	1	2	:	:	:	:	:	:	:	2	:	1	:	:	:	:	:	6
				M	:	:	:	:	:	:	1	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:
				N	:	:	:	:	:	:	:	:	:	4	:	:	:	:	:	:	:	:	1	:	:	:	:
				P	1	:	2	:	:	:	:	:	:	:	:	:	:	:	2	a	:	:	:	4	:	:	:
				Q	:	1	:	1	:	:	:	:	1	:	1	:	:	2	1	:	1	:	1	:	2	1	:
				R	:	:	:	:	:	:	:	:	2	:	2	:	:	1	1	:	:	2	:	:	:	2	:
				S	:	1	:	:	:	:	:	:	:	:	1	:	:	2	1	:	:	:	1	2	1	1	:
				T	:	:	3	5	:	:	:	:	:	:	:	2	:	:	:	:	2	4	:	:	:	:	:
				V	:	:	1	1	3	:	4	:	1	:	:	3	:	:	1	:	4	:	:	:	:	:	2
				W	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				Y	:	:	:	:	2	9	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:
.
			bits	6.3
				5.6
				5.0
				4.4
			Information	3.8
			content	3.1
			(59.4 bits)	2.5
				1.9
				1.3
				0.6
				0.0
.
			Multilevel		`G`	`K`	`T`	`T`	`A`	`Y`	`V`	`C`	`E`	`G`	`F`	`A`	`C`	`D`	`L`	`P`	`V`	`T`	`D`	`P`	`A`	`E`	`L`
			consensus		`D`	`G`	`P`	`A`	`V`		`I`		`H`	`N`	`R`	`V`		`Q`	`P`		`T`	`R`		`I`	`D`	`R`	`A`
			sequence						`Y`		`L`		`R`			`T`		`S`						`S`	`E`		`V`
																									`Q`

.

D.melanogaster	773	7.77e-24	`RLQTKFKMVG`		`G`	`K`	`T`	`T`	`V`	`Y`	`I`	`C`	`H`	`E`	`R`	`A`	`C`	`R`	`M`	`P`	`V`	`T`	`D`	`P`	`Q`	`Q`	`L`	`EDNLMAYFFS`
B.subtilis	658	2.20e-21	`PFAADYRIID`		`G`	`K`	`T`	`T`	`V`	`Y`	`I`	`C`	`E`	`N`	`F`	`A`	`C`	`Q`	`Q`	`P`	`T`	`T`	`N`	`I`	`E`	`E`	`A`	`IHTLISSRD`
H.sapiens	758	1.85e-20	`PFLSTLRRLE`		`D`	`Q`	`A`	`T`	`A`	`Y`	`V`	`C`	`E`	`N`	`Q`	`A`	`C`	`S`	`V`	`P`	`I`	`T`	`D`	`P`	`C`	`E`	`L`	`RKLLHP`
D.radiodaurans	661	3.38e-19	`GDLPVLEARP`		`G`	`G`	`G`	`Q`	`A`	`Y`	`V`	`C`	`V`	`N`	`H`	`A`	`C`	`Q`	`L`	`P`	`T`	`R`	`D`	`P`	`A`	`E`	`L`	`ARQVAAL`
A.aeolicus	660	9.57e-18	`ENLEQMKPVE`		`G`	`K`	`T`	`T`	`Y`	`Y`	`L`	`C`	`R`	`N`	`Y`	`T`	`C`	`E`	`S`	`P`	`Q`	`I`	`Q`	`S`	`D`	`K`	`V`	`LERIKGKGKG`
C.elegans	700	3.49e-17	`GPSHKAMAEG`		`P`	`K`	`P`	`A`	`V`	`Y`	`M`	`C`	`K`	`G`	`F`	`V`	`C`	`D`	`R`	`P`	`V`	`K`	`A`	`I`	`Q`	`E`	`L`	`EELFNKF`
M.thermoautotrophicum	648	1.00e-16	`AHLNEKVALG`		`D`	`G`	`C`	`T`	`Y`	`Y`	`L`	`C`	`D`	`G`	`S`	`K`	`C`	`H`	`P`	`P`	`A`	`E`	`D`	`P`	`E`	`R`	`V`	`IEYLGVK`
M.tuberculosis	643	2.52e-16	`ALLVGRDRVA`		`G`	`A`	`D`	`A`	`A`	`Y`	`V`	`C`	`R`	`G`	`R`	`V`	`C`	`D`	`L`	`P`	`V`	`T`	`S`	`A`	`A`	`E`	`L`	`ATALGVPG`
A.pernix	647	3.62e-16	`EYAASMTTMG`		`G`	`S`	`P`	`A`	`F`	`Y`	`I`	`C`	`H`	`G`	`G`	`V`	`C`	`K`	`E`	`P`	`L`	`R`	`D`	`E`	`D`	`R`	`A`	`LEEVMRLSKK`
A.thaliana	837	1.05e-15	`AEMAKKNRNS`		`E`	`K`	`V`	`V`	`A`	`L`	`V`	`C`	`Q`	`H`	`F`	`T`	`C`	`S`	`P`	`P`	`V`	`F`	`D`	`S`	`S`	`S`	`L`	`TRLLSK`

Motif 8 block diagrams

Name

Lowest
p-value

Motifs

D.melanogaster

7.8e-24

B.subtilis

2.2e-21

H.sapiens

1.9e-20

D.radiodaurans

3.4e-19

A.aeolicus

9.6e-18

C.elegans

3.5e-17

M.thermoautotrophicum

1e-16

M.tuberculosis

2.5e-16

A.pernix

3.6e-16

A.thaliana

1e-15

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775	800	825	850

Motif 8 in BLOCKS format

BL   MOTIF 8 width=23 seqs=10
D.melanogaster           (  773) GKTTVYICHERACRMPVTDPQQL  1 
B.subtilis               (  658) GKTTVYICENFACQQPTTNIEEA  1 
H.sapiens                (  758) DQATAYVCENQACSVPITDPCEL  1 
D.radiodaurans           (  661) GGGQAYVCVNHACQLPTRDPAEL  1 
A.aeolicus               (  660) GKTTYYLCRNYTCESPQIQSDKV  1 
C.elegans                (  700) PKPAVYMCKGFVCDRPVKAIQEL  1 
M.thermoautotrophicum    (  648) DGCTYYLCDGSKCHPPAEDPERV  1 
M.tuberculosis           (  643) GADAAYVCRGRVCDLPVTSAAEL  1 
A.pernix                 (  647) GSPAFYICHGGVCKEPLRDEDRA  1 
A.thaliana               (  837) EKVVALVCQHFTCSPPVFDSSSL  1 
//

Motif 8 position-specific scoring matrix

log-odds matrix: alength= 20 w= 23 n= 7773 bayes= 11.0756 E= 3.8e-038 
  -252   -310     82    -23   -466    324   -281   -400   -246   -490   -379    -84      2   -211   -320   -199   -266   -387   -439   -406 
     2   -235   -158   -123   -325    100   -137   -237    282   -291   -195    -47   -250    152    -88     61   -107   -234   -345   -261 
    13    241     34   -185   -258     11   -189   -130   -118   -229   -144   -105    178    -89   -191    -99    237     54   -323   -257 
   128   -143   -342   -323   -321   -287   -302   -169   -242   -301   -195   -169   -330    118   -294    -68    340     46   -381   -348 
   182   -132   -435   -397    110   -343   -227    -43   -317   -162   -101   -257   -362   -256   -334   -225   -161    207   -200    217 
  -451   -309   -517   -529    -30   -507   -188   -272   -445     -9   -272   -345   -482   -361   -437   -396   -392   -336   -155    440 
  -324   -218   -504   -497   -237   -486   -446    330   -415     73    157   -368   -466   -376   -458   -374   -242    240   -398   -350 
  -411    622   -546   -531   -488   -544   -492   -368   -524   -497   -393   -438   -533   -469   -500   -444   -359   -455   -580   -555 
  -136   -222     46    104   -283   -219    217   -202    102   -256   -156    -28   -211    152    130    -76    -72     28   -314   -224 
  -310   -332    -84     25   -466    224    158   -454   -201   -509   -439    349   -339   -171   -306   -135   -197   -450   -506   -365 
  -156   -154   -177   -143    206    -37    128   -157    -74   -216   -138    -73   -233    102     85     23   -109   -174   -162    249 
   201   -103   -320   -277   -249   -246   -259    -87     55   -213   -137   -189   -317   -172   -241   -125    171    195   -326   -280 
  -411    622   -546   -531   -488   -544   -492   -368   -524   -497   -393   -438   -533   -469   -500   -444   -359   -455   -580   -555 
  -131   -217    120     40   -277   -212    130   -197    100   -252   -152    -19   -206    221     57    129    -67   -194   -309   -219 
  -129   -181   -137     30   -240   -218   -111   -133    -24     43    147    -33    143    146     51     59    -64     39   -290   -207 
  -337   -374   -448   -460   -498   -436   -426   -430   -390   -475   -450   -387    432   -347   -435   -332   -344   -428   -541   -529 
   -30    -87   -371   -339   -185   -330   -261    128   -273    -36    -78   -235   -304     58   -287   -217    122    304   -287   -248 
  -148   -194   -156     26     56   -235   -123     87     99   -230   -137    -47   -229    -12    131    -84    261   -163   -304   -224 
  -168   -309    369   -133   -420   -333   -255   -348   -305   -443   -364     62   -414    -34   -361   -103   -292   -365   -428   -375 
   -31   -226   -265    -36   -332   -298   -253    136   -187   -298   -242   -189    348   -151   -253     88   -166   -233   -405   -352 
    73    224    126    109   -290   -217   -114   -209    -25   -265   -165    -23   -215    223   -111     61    -78   -205   -323   -232 
  -206   -293   -153    228   -371   -284   -163   -266    115   -316   -221    -94   -277    156    150     52   -144   -262   -375   -297 
    70   -192   -526   -480   -207   -435   -400     -3   -405    246    -75   -364   -423   -330   -416   -327   -229    158   -365   -331

Motif 8 position-specific probability matrix

letter-probability matrix: alength= 20 w= 23 n= 7773 E= 3.8e-038 
 0.016052  0.001508  0.106898  0.068227  0.001759  0.675109  0.004083  0.002454  0.009684  0.003412  0.001738  0.017594  0.047830  0.007372  0.006441  0.015475  0.007190  0.004044  0.000840  0.002291 
 0.093153  0.002533  0.020233  0.033909  0.004667  0.142710  0.011063  0.007573  0.375112  0.013549  0.006250  0.022673  0.008361  0.091197  0.032230  0.093654  0.021525  0.011752  0.001611  0.006245 
 0.100767  0.068445  0.076871  0.022120  0.007438  0.077152  0.007679  0.015912  0.023525  0.020845  0.008864  0.015114  0.162107  0.017124  0.015796  0.030962  0.234993  0.085975  0.001884  0.006426 
 0.223795  0.004791  0.005689  0.008497  0.004801  0.009761  0.003512  0.012188  0.009905  0.012708  0.006226  0.009761  0.004775  0.071829  0.007737  0.038317  0.479197  0.081824  0.001259  0.003427 
 0.324414  0.005157  0.002985  0.005091  0.095019  0.006649  0.005936  0.029020  0.005899  0.033133  0.011964  0.005294  0.003845  0.005374  0.005852  0.012916  0.014808  0.249904  0.004399  0.172341 
 0.004036  0.001516  0.001680  0.002040  0.036117  0.002125  0.007777  0.005957  0.002428  0.096104  0.003656  0.002879  0.001665  0.002606  0.002854  0.003964  0.002987  0.005771  0.006015  0.807823 
 0.009725  0.002848  0.001841  0.002541  0.008625  0.002457  0.001298  0.386647  0.002987  0.169044  0.071713  0.002453  0.001870  0.002349  0.002480  0.004611  0.008438  0.313572  0.001114  0.003386 
 0.005347  0.961850  0.001376  0.002007  0.001504  0.001651  0.000943  0.003060  0.001407  0.003251  0.001584  0.001508  0.001174  0.001233  0.001850  0.002827  0.003767  0.002529  0.000317  0.000816 
 0.035905  0.002764  0.083444  0.164524  0.006231  0.015657  0.128450  0.009690  0.107908  0.017305  0.008144  0.025870  0.010891  0.091017  0.146200  0.036298  0.027419  0.072185  0.002006  0.008092 
 0.010707  0.001292  0.033883  0.095120  0.001761  0.337556  0.085168  0.001692  0.013170  0.003000  0.001151  0.352240  0.004511  0.009688  0.007098  0.024231  0.011535  0.002621  0.000527  0.003048 
 0.031245  0.004432  0.017758  0.029606  0.184924  0.055184  0.069159  starts: w=8, seq=0, l=865          
starts: w=8, seq=5, l=677          
starts: w=8, seq=10, l=681          
starts: w=11, seq=0, l=865          
starts: w=11, seq=5, l=677          
starts: w=11, seq=10, l=681          
starts: w=15, seq=0, l=865          
starts: w=15, seq=5, l=677          
starts: w=15, seq=10, l=681          
starts: w=21, seq=0, l=865          
starts: w=21, seq=5, l=677          
starts: w=21, seq=10, l=681          
starts: w=29, seq=0, l=865          
starts: w=29, seq=5, l=677          
starts: w=29, seq=10, l=681          
starts: w=41, seq=0, l=865          
starts: w=41, seq=5, l=677          
starts: w=41, seq=10, l=681          
starts: w=50, seq=0, l=865          
starts: w=50, seq=5, l=677          
starts: w=50, seq=10, l=681          

em: w=   8, psites=   2, iter=   0 
em: w=   8, psites=   2, iter=  10 
em: w=   8, psites=   2, iter=  20 
em: w=   8, psites=   2, iter=  30 
em: w=   8, psites=   2, iter=  40 
em: w=   8, psites=   4, iter=   0 
em: w=   8, psites=   4, iter=  10 
em: w=   8, psites=   4, iter=  20 
em: w=   8, psites=   4, iter=  30 
em: w=   8, psites=   4, iter=  40 
em: w=   8, psites=   8, iter=   0 
em: w=   8, psites=   8, iter=  10 
em: w=   8, psites=   8, iter=  20 
em: w=   8, psites=   8, iter=  30 
em: w=   8, psites=   8, iter=  40 
em: w=   8, psites=  12, iter=   0 
em: w=   8, psites=  12, iter=  10 
em: w=   8, psites=  12, iter=  20 
em: w=  11, psites=   2, iter=   0 
em: w=  11, psites=   2, iter=  10 
em: w=  11, psites=   2, iter=  20 
em: w=  11, psites=   2, iter=  30 
em: w=  11, psites=   2, iter=  40 
em: w=  11, psites=   4, iter=   0 
em: w=  11, psites=   4, iter=  10 
em: w=  11, psites=   4, iter=  20 
em: w=  11, psites=   4, iter=  30 
em: w=  11, psites=   4, iter=  40 
em: w=  11, psites=   8, iter=   0 
em: w=  11, psites=   8, iter=  10 
em: w=  11, psites=   8, iter=  20 
em: w=  11, psites=   8, iter=  30 
em: w=  11, psites=   8, iter=  40 
em: w=  11, psites=  12, iter=   0 
em: w=  11, psites=  12, iter=  10 
em: w=  11, psites=  12, iter=  20 
em: w=  11, psites=  12, iter=  30 
em: w=  11, psites=  12, iter=  40 
em: w=  15, psites=   2, iter=   0 
em: w=  15, psites=   2, iter=  10 
em: w=  15, psites=   2, iter=  20 
em: w=  15, psites=   2, iter=  30 
em: w=  15, psites=   2, iter=  40 
em: w=  15, psites=   4, iter=   0 
em: w=  15, psites=   8, iter=   0 
em: w=  15, psites=   8, iter=  10 
em: w=  15, psites=   8, iter=  20 
em: w=  15, psites=   8, iter=  30 
em: w=  15, psites=   8, iter=  40 
em: w=  15, psites=  12, iter=   0 
em: w=  21, psites=   2, iter=   0 
em: w=  21, psites=   4, iter=   0 
em: w=  21, psites=   4, iter=  10 
em: w=  21, psites=   4, iter=  20 
em: w=  21, psites=   4, iter=  30 
em: w=  21, psites=   4, iter=  40 
em: w=  21, psites=   8, iter=   0 
em: w=  21, psites=   8, iter=  10 
em: w=  21, psites=   8, iter=  20 
em: w=  21, psites=   8, iter=  30 
em: w=  21, psites=   8, iter=  40 
em: w=  21, psites=  12, iter=   0 
em: w=  29, psites=   2, iter=   0 
em: w=  29, psites=   4, iter=   0 
em: w=  29, psites=   4, iter=  10 
em: w=  29, psites=   8, iter=   0 
em: w=  29, psites=   8, iter=  10 
em: w=  29, psites=   8, iter=  20 
em: w=  29, psites=  12, iter=   0 
em: w=  41, psites=   2, iter=   0 
em: w=  41, psites=   2, iter=  10 
em: w=  41, psites=   2, iter=  20 
em: w=  41, psites=   2, iter=  30 
em: w=  41, psites=   2, iter=  40 
em: w=  41, psites=   4, iter=   0 
em: w=  41, psites=   4, iter=  10 
em: w=  41, psites=   4, iter=  20 
em: w=  41, psites=   4, iter=  30 
em: w=  41, psites=   4, iter=  40 
em: w=  41, psites=   8, iter=   0 
em: w=  41, psites=  12, iter=   0 
em: w=  50, psites=   2, iter=   0 
em: w=  50, psites=   4, iter=   0 
em: w=  50, psites=   8, iter=   0 
em: w=  50, psites=  12, iter=   0 0.013207  0.031710  0.022847  0.009229  0.018903  0.009401  0.064363  0.107052  0.072232  0.021218  0.017730  0.005727  0.214070 
 0.371668  0.006302  0.006627  0.011710  0.007933  0.013017  0.004749  0.021486  0.077912  0.023344  0.009308  0.008475  0.005241  0.009621  0.011133  0.025919  0.148607  0.229622  0.001843  0.005482 
 0.005347  0.961850  0.001376  0.002007  0.001504  0.001651  0.000943  0.003060  0.001407  0.003251  0.001584  0.001508  0.001174  0.001233  0.001850  0.002827  0.003767  0.002529  0.000317  0.000816 
 0.037211  0.002877  0.139670  0.105209  0.006510  0.016436  0.070440  0.009989  0.106595  0.017806  0.008401  0.027440  0.011283  0.147238  0.087676  0.150763  0.028535  0.015449  0.002071  0.008399 
 0.037645  0.003691  0.023559  0.098421  0.008426  0.015750  0.013237  0.015639  0.045058  0.137149  0.066527  0.024937  0.127041  0.087550  0.084591  0.092484  0.029026  0.077814  0.002367  0.009088 
 0.008927  0.000963  0.002721  0.003284  0.001412  0.003481  0.001487  0.001991  0.003567  0.003784  0.001064  0.002144  0.944627  0.002868  0.002900  0.006167  0.004172  0.003049  0.000414  0.000979 
 0.075014  0.007085  0.004649  0.007620  0.012293  0.007242  0.004669  0.095151  0.007999  0.079598  0.014034  0.006179  0.005718  0.047353  0.008087  0.013649  0.105165  0.489252  0.002405  0.006840 
 0.033104  0.003373  0.020520  0.095480  0.065414  0.014016  0.012141  0.071850  0.105532  0.020655  0.009287  0.022702  0.009676  0.029235  0.147157  0.034467  0.276006  0.019168  0.002145  0.008073 
 0.028714  0.001520  0.781540  0.031662  0.002425  0.007129  0.004865  0.003505  0.006401  0.004725  0.001930  0.048190  0.002677  0.025141  0.004849  0.030237  0.006004  0.004731  0.000909  0.002846 
 0.074083  0.002689  0.009657  0.062129  0.004436  0.009060  0.004936  0.101022  0.014552  0.012917  0.004498  0.008494  0.526590  0.011137  0.010249  0.112996  0.014353  0.011803  0.001066  0.003335 
 0.152315  0.061043  0.145651  0.170191  0.005960  0.015886  0.012926  0.009232  0.044712  0.016310  0.007666  0.026820  0.010591  0.148898  0.027356  0.094097  0.026431  0.014370  0.001874  0.007669 
 0.022107  0.001695  0.021054  0.386334  0.003395  0.009961  0.009216  0.006213  0.118219  0.011437  0.005188  0.016345  0.006931  0.093415  0.167704  0.088267  0.016698  0.009622  0.001307  0.004892 
 0.149159  0.003413  0.001584  0.002873  0.010607  0.003514  0.001785  0.038410  0.003201  0.561813  0.014276  0.002522  0.002519  0.003230  0.003310  0.006403  0.009277  0.176858  0.001405  0.003844






Time 207.72 secs.

P N
MOTIF 9 width = 21 sites = 11 llr = 410 E-value = 3.7e-037

NAME	START	P-VALUE				SITES
			Simplified	A	:	:	3	:	1	:	1	:	1	3	6	:	:	a	:	1	:	:	:	:	:
			pos.-specific	C	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
			probability	D	:	:	:	:	3	1	:	:	:	:	:	:	a	:	9	:	1	:	:	1	:
			matrix	E	:	:	:	1	4	:	:	:	:	:	:	4	:	:	1	:	2	3	4	5	2
				F	:	:	:	:	:	:	:	9	2	:	:	:	:	:	:	:	1	:	1	:	:
				G	1	:	:	:	1	8	7	:	:	:	1	:	:	:	:	:	3	4	1	:	7
				H	:	:	4	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	3	:
				I	1	1	:	:	:	:	:	1	:	:	:	:	:	:	:	1	:	:	:	:	:
				K	:	2	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				L	3	3	:	:	1	:	:	:	:	:	:	2	:	:	:	:	2	:	1	:	:
				M	4	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				N	:	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	1
				P	:	:	:	5	:	:	:	:	:	:	:	:	:	:	:	:	2	3	:	:	:
				Q	:	:	:	:	:	:	:	:	:	:	:	2	:	:	:	:	:	:	:	:	:
				R	:	1	:	1	:	1	:	:	:	:	:	:	:	:	:	:	:	:	1	1	:
				S	1	2	3	:	1	:	1	:	:	7	3	:	:	:	:	5	:	:	:	:	:
				T	:	1	:	1	:	:	:	:	1	:	:	:	:	:	:	3	:	1	1	:	:
				V	:	:	:	:	:	:	:	:	:	:	:	2	:	:	:	:	:	:	1	:	:
				W	1	:	1	:	:	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:
				Y	:	:	:	:	:	:	:	:	6	:	:	:	:	:	:	:	:	:	:	:	:
.
			bits	6.3
				5.6
				5.0
				4.4
			Information	3.8
			content	3.1
			(53.8 bits)	2.5
				1.9
				1.3
				0.6
				0.0
.
			Multilevel		`M`	`L`	`H`	`P`	`E`	`G`	`G`	`F`	`Y`	`S`	`A`	`E`	`D`	`A`	`D`	`S`	`G`	`G`	`E`	`E`	`G`
			consensus		`L`		`A`		`D`					`A`	`S`					`T`		`E`		`H`
			sequence				`S`															`P`


.

D.radiodaurans	313	3.91e-21	`RETLAYLERE`		`M`	`L`	`A`	`P`	`D`	`G`	`G`	`F`	`Y`	`S`	`A`	`Q`	`D`	`A`	`D`	`T`	`P`	`T`	`E`	`H`	`G`	`GVEGLTFTWT`
A.aeolicus	307	7.14e-20	`YEIVDFLKRD`		`M`	`L`	`S`	`P`	`E`	`G`	`A`	`F`	`Y`	`S`	`A`	`W`	`D`	`A`	`D`	`S`	`E`	`G`	`E`	`E`	`G`	`KFYTWSFEEL`
H.sapiens	372	1.17e-18	`KGILQYVARS`		`L`	`S`	`H`	`R`	`S`	`G`	`G`	`F`	`Y`	`S`	`A`	`E`	`D`	`A`	`D`	`S`	`P`	`P`	`E`	`R`	`G`	`QRPKEGAYYV`
M.thermoautotrophicum	305	2.77e-18	`LEISEYVLRD`		`L`	`K`	`S`	`P`	`E`	`G`	`G`	`F`	`Y`	`S`	`A`	`V`	`D`	`A`	`E`	`S`	`G`	`G`	`V`	`E`	`G`	`GYYLWRASEI`
C.elegans	324	9.10e-18	`INDIYQYMQK`		`I`	`S`	`H`	`K`	`D`	`G`	`G`	`F`	`Y`	`A`	`A`	`E`	`D`	`A`	`D`	`S`	`L`	`P`	`N`	`H`	`N`	`SSNKVEGAFC`
A.thaliana	467	9.95e-18	`RDILDYLRRD`		`M`	`I`	`A`	`P`	`E`	`G`	`G`	`I`	`F`	`S`	`A`	`E`	`D`	`A`	`D`	`S`	`F`	`E`	`F`	`E`	`G`	`AKRKKEGAFY`
B.subtilis	309	5.13e-17	`EQIITFIQRE`		`M`	`T`	`H`	`E`	`D`	`G`	`S`	`F`	`F`	`S`	`A`	`L`	`D`	`A`	`D`	`T`	`E`	`G`	`E`	`E`	`G`	`KYYVWSKEEI`
D.melanogaster	384	3.58e-16	`DKIHKYLIKD`		`L`	`R`	`H`	`P`	`L`	`G`	`G`	`F`	`Y`	`A`	`G`	`E`	`D`	`A`	`D`	`S`	`L`	`P`	`T`	`H`	`E`	`DKVKVEGAFY`
A.fulgidus	304	2.66e-14	`DGIVEYYRKF`		`G`	`C`	`S`	`N`	`E`	`G`	`G`	`F`	`Y`	`A`	`S`	`Q`	`D`	`A`	`D`	`I`	`G`	`E`	`L`	`D`	`E`	`GGYYLFSDRE`
A.pernix	299	5.99e-14	`AVSTLEFAMS`		`W`	`L`	`W`	`T`	`G`	`R`	`G`	`F`	`A`	`S`	`S`	`V`	`D`	`A`	`D`	`T`	`G`	`E`	`G`	`E`	`G`	`AYYTFTLEEA`
M.tuberculosis	309	1.85e-12	`TARFLLDELG`		`S`	`K`	`A`	`P`	`A`	`D`	`M`	`F`	`T`	`S`	`S`	`L`	`D`	`A`	`D`	`A`	`D`	`G`	`R`	`E`	`G`	`STYVWTPVQL`

Motif 9 block diagrams

Name

Lowest
p-value

Motifs

D.radiodaurans

3.9e-21

A.aeolicus

7.1e-20

H.sapiens

1.2e-18

M.thermoautotrophicum

2.8e-18

C.elegans

9.1e-18

A.thaliana

9.9e-18

B.subtilis

5.1e-17

D.melanogaster

3.6e-16

A.fulgidus

2.7e-14

A.pernix

6e-14

M.tuberculosis

1.8e-12

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775	800	825	850

Motif 9 in BLOCKS format

BL   MOTIF 9 width=21 seqs=11
D.radiodaurans           (  313) MLAPDGGFYSAQDADTPTEHG  1 
A.aeolicus               (  307) MLSPEGAFYSAWDADSEGEEG  1 
H.sapiens                (  372) LSHRSGGFYSAEDADSPPERG  1 
M.thermoautotrophicum    (  305) LKSPEGGFYSAVDAESGGVEG  1 
C.elegans                (  324) ISHKDGGFYAAEDADSLPNHN  1 
A.thaliana               (  467) MIAPEGGIFSAEDADSFEFEG  1 
B.subtilis               (  309) MTHEDGSFFSALDADTEGEEG  1 
D.melanogaster           (  384) LRHPLGGFYAGEDADSLPTHE  1 
A.fulgidus               (  304) GCSNEGGFYASQDADIGELDE  1 
A.pernix                 (  299) WLWTGRGFASSVDADTGEGEG  1 
M.tuberculosis           (  309) SKAPADMFTSSLDADADGREG  1 
//

Motif 9 position-specific scoring matrix

log-odds matrix: alength= 20 w= 21 n= 7797 bayes= 9.3658 E= 3.7e-037 
  -174    -86   -401   -349   -141     -7   -249    139   -267    126    343   -219   -311   -210   -287     30   -101    -23    184   -193 
  -158    229   -237   -190   -184   -268   -176    116    141    105    -72   -114   -265    -85     35    118     88    -69   -265   -204 
   147   -169   -313   -318   -320   -254    343   -284   -243   -369   -282   -178   -337   -206   -301    198   -174   -259    208   -277 
  -185   -258   -226    -25   -352   -289   -208   -265     44   -317   -249     92    352   -100     11   -151     45   -263   -399   -331 
   -12   -309    185    200   -372      1   -184   -276    -88    -52   -236    -78   -267    -39   -188     44   -145   -266   -405   -310 
  -240   -287    -90   -369   -459    358   -344   -395   -303   -506   -376   -172   -390   -324    -99   -231   -320   -386   -408   -421 
   -94   -266   -296   -381   -460    351   -354   -393   -314   -503     33   -186   -387   -331   -340    -56   -303   -375   -415   -428 
  -368   -183   -460   -473    426   -467   -399    -54   -429   -171   -188   -368   -396   -406   -470   -313   -363   -243   -218    -79 
   -83   -120   -280   -274    189   -312      6   -145   -223   -200   -141   -177   -273   -197   -243   -163    -16   -176    -91    381 
   153   -154   -494   -532   -491   -255   -472   -426   -482   -509   -402   -307   -369   -385   -472    344   -150   -324   -526   -519 
   279    -89   -439   -437   -395      7   -414   -306   -394   -388   -290   -300   -381   -336   -406    174   -180   -197   -437   -446 
  -170   -149   -201    176   -202   -279   -187    -62   -111     57    -91   -121   -272    211   -184   -148   -104    134    181   -219 
  -369   -324    387   -149   -436   -385   -293   -363   -379   -463   -387    -42   -457   -313   -409   -313   -347   -383   -438   -400 
   334   -190   -520   -529   -477   -310   -489   -392   -482   -474   -387   -398   -461   -427   -490   -208   -284   -295   -506   -517 
  -352   -310    383    -91   -421   -372   -277   -346   -362   -448   -370    -25   -445   -295   -393   -296   -331   -366   -425   -385 
   -96   -123   -340   -406   -345   -316   -327    -44   -273   -377   -264   -110   -309   -270   -298    339    203   -324   -388   -344 
  -155   -219     41     99     48    136   -135   -180    -50     34   -161    -42    146    -22   -135    -98    -93   -188   -327   -239 
  -215   -279   -132    165   -445    201   -249   -354   -181   -417   -330    -83    230   -125   -283   -167     81   -327   -484   -391 
  -135   -190   -141    167     46     -7   -116   -145    -29    -44   -130    130   -217     -7     44    -81     84     31   -298   -213 
  -259   -451     74    264   -512   -329    284   -372   -151   -428   -337   -135   -323    -73     35   -229   -233   -346   -535   -427 
  -248   -294   -239    -21   -463    348   -319   -403   -290   -509   -385     45   -385   -296   -332   -219   -302   -393   -420   -417

Motif 9 position-specific probability matrix

letter-probability matrix: alength= 20 w= 21 n= 7797 E= 3.7e-037 
 0.027511  0.007097  0.003769  0.007106  0.016749  0.067878  0.005080  0.103048  0.008350  0.243585  0.260047  0.006885  0.005449  0.007407  0.008110  0.075773  0.022568  0.050609  0.062966  0.010013 
 0.030783  0.062938  0.011709  0.021390  0.012395  0.011125  0.008450  0.087408  0.140880  0.210933  0.014597  0.014298  0.007520  0.017584  0.075720  0.139872  0.083535  0.036774  0.002808  0.009280 
 0.254550  0.003999  0.006948  0.008780  0.004845  0.012273  0.306930  0.005482  0.009836  0.007930  0.003418  0.009171  0.004562  0.007619  0.007359  0.242700  0.013533  0.009864  0.074601  0.005600 
 0.025524  0.002155  0.012692  0.067020  0.003884  0.009671  0.006742  0.006254  0.072301  0.011362  0.004293  0.059303  0.540827  0.015888  0.063956  0.021585  0.062015  0.009574  0.001107  0.003847 
 0.084775  0.001518  0.219332  0.319881  0.003375  0.071761  0.007987  0.005808  0.028840  0.070984  0.004686  0.018346  0.007409  0.024303  0.016069  0.083421  0.016567  0.009410  0.001064  0.004464 
 0.017400  0.001760  0.032526  0.006187  0.001846  0.853371  0.002628  0.002544  0.006511  0.003054  0.001775  0.009523  0.003167  0.003356  0.029813  0.012425  0.004922  0.004087  0.001041  0.002064 
 0.047878  0.002040  0.007827  0.005705  0.001832  0.814980  0.002447  0.002566  0.006009  0.003119  0.030226  0.008673  0.003220  0.003211  0.005597  0.041753  0.005528  0.004422  0.000996  0.001970 
 0.007169  0.003628  0.002509  0.003017  0.854259  0.002802  0.001792  0.026939  0.002718  0.031286  0.006556  0.002458  0.003027  0.001905  0.002276  0.007010  0.003647  0.011003  0.003881  0.022117 
 0.051921  0.005621  0.008702  0.011972  0.164653  0.008214  0.029696  0.014359  0.011319  0.025469  0.009051  0.009178  0.007103  0.008086  0.010984  0.019859  0.040564  0.017492  0.009399  0.536359 
 0.266738  0.004446  0.001976  0.001993  0.001473  0.012220  0.001081  0.002042  0.001887  0.002997  0.001489  0.003730  0.003650  0.002211  0.002248  0.665949  0.016068  0.006292  0.000461  0.001050 
 0.637998  0.006957  0.002889  0.003849  0.002869  0.074824  0.001620  0.004706  0.003469  0.006934  0.003227  0.003920  0.003354  0.003098  0.003537  0.205955  0.013018  0.015185  0.000852  0.001740 
 0.028277  0.004585  0.015109  0.270504  0.010929  0.010335  0.007833  0.025578  0.024651  0.151388  0.012773  0.013534  0.007142  0.136772  0.016554  0.022134  0.021965  0.149865  0.061690  0.008381 
 0.007132  0.001363  0.888432  0.028371  0.002159  0.004951  0.003743  0.003163  0.003841  0.004111  0.001647  0.023440  0.001990  0.003637  0.003479  0.007044  0.004092  0.004175  0.000844  0.002388 
 0.934277  0.003453  0.001652  0.002034  0.001627  0.008312  0.000966  0.002595  0.001884  0.003818  0.001642  0.001989  0.001934  0.001647  0.001984  0.014593  0.006327  0.007678  0.000527  0.001062 
 0.008012  0.001502  0.864263  0.042573  0.002394  0.005421  0.004186  0.003557  0.004316  0.004583  0.001855  0.026467  0.002160  0.004106  0.003872  0.007884  0.004570  0.004695  0.000928  0.002655 
 0.047238  0.005513  0.005739  0.004795  0.004055  0.008019  0.002966  0.028882  0.008027  0.007454  0.003868  0.014661  0.005543  0.004903  0.007501  0.644916  0.184895  0.006294  0.001200  0.003530 
 0.031447  0.002819  0.080777  0.158164  0.062062  0.183283  0.011197  0.011229  0.037656  0.129094  0.007871  0.023508  0.130108  0.027228  0.023220  0.031232  0.023850  0.016131  0.001829  0.007295 
 0.020798  0.001864  0.024367  0.250343  0.002028  0.288826  0.005066  0.003375  0.015118  0.005671  0.002449  0.017715  0.232571  0.013403  0.008309  0.019285  0.079501  0.006149  0.000617  0.002547 
 0.036045  0.003451  0.022917  0.253607  0.061014  0.068308  0.012791  0.014374  0.043517  0.075037  0.009791  0.077349  0.010494  0.030339  0.080577  0.035154  0.080985  0.073301  0.002241  0.008710 
 0.015307  0.000567  0.101526  0.498starts: w=8, seq=0, l=865          
starts: w=8, seq=5, l=677          
starts: w=8, seq=10, l=681          
starts: w=11, seq=0, l=865          
starts: w=11, seq=5, l=677          
starts: w=11, seq=10, l=681          
starts: w=15, seq=0, l=865          
starts: w=15, seq=5, l=677          
starts: w=15, seq=10, l=681          
starts: w=21, seq=0, l=865          
starts: w=21, seq=5, l=677          
starts: w=21, seq=10, l=681          
starts: w=29, seq=0, l=865          
starts: w=29, seq=5, l=677          
starts: w=29, seq=10, l=681          
starts: w=41, seq=0, l=865          
starts: w=41, seq=5, l=677          
starts: w=41, seq=10, l=681          
starts: w=50, seq=0, l=865          
starts: w=50, seq=5, l=677          
starts: w=50, seq=10, l=681          

em: w=   8, psites=   2, iter=   0 
em: w=   8, psites=   2, iter=  10 
em: w=   8, psites=   2, iter=  20 
em: w=   8, psites=   2, iter=  30 
em: w=   8, psites=   2, iter=  40 
em: w=   8, psites=   4, iter=   0 
em: w=   8, psites=   4, iter=  10 
em: w=   8, psites=   4, iter=  20 
em: w=   8, psites=   4, iter=  30 
em: w=   8, psites=   4, iter=  40 
em: w=   8, psites=   8, iter=   0 
em: w=   8, psites=   8, iter=  10 
em: w=   8, psites=   8, iter=  20 
em: w=   8, psites=   8, iter=  30 
em: w=   8, psites=   8, iter=  40 
em: w=   8, psites=  12, iter=   0 
em: w=   8, psites=  12, iter=  10 
em: w=   8, psites=  12, iter=  20 
em: w=   8, psites=  12, iter=  30 
em: w=   8, psites=  12, iter=  40 
em: w=  11, psites=   2, iter=   0 
em: w=  11, psites=   2, iter=  10 
em: w=  11, psites=   2, iter=  20 
em: w=  11, psites=   2, iter=  30 
em: w=  11, psites=   2, iter=  40 
em: w=  11, psites=   4, iter=   0 
em: w=  11, psites=   4, iter=  10 
em: w=  11, psites=   4, iter=  20 
em: w=  11, psites=   8, iter=   0 
em: w=  11, psites=   8, iter=  10 
em: w=  11, psites=   8, iter=  20 
em: w=  11, psites=   8, iter=  30 
em: w=  11, psites=   8, iter=  40 
em: w=  11, psites=  12, iter=   0 
em: w=  11, psites=  12, iter=  10 
em: w=  11, psites=  12, iter=  20 
em: w=  11, psites=  12, iter=  30 
em: w=  11, psites=  12, iter=  40 
em: w=  15, psites=   2, iter=   0 
em: w=  15, psites=   4, iter=   0 
em: w=  15, psites=   8, iter=   0 
em: w=  15, psites=   8, iter=  10 
em: w=  15, psites=   8, iter=  20 
em: w=  15, psites=   8, iter=  30 
em: w=  15, psites=   8, iter=  40 
em: w=  15, psites=  12, iter=   0 
em: w=  15, psites=  12, iter=  10 
em: w=  15, psites=  12, iter=  20 
em: w=  15, psites=  12, iter=  30 
em: w=  15, psites=  12, iter=  40 
em: w=  21, psites=   2, iter=   0 
em: w=  21, psites=   4, iter=   0 
em: w=  21, psites=   4, iter=  10 
em: w=  21, psites=   8, iter=   0 
em: w=  21, psites=  12, iter=   0 
em: w=  21, psites=  12, iter=  10 
em: w=  21, psites=  12, iter=  20 
em: w=  21, psites=  12, iter=  30 
em: w=  21, psites=  12, iter=  40 
em: w=  29, psites=   2, iter=   0 
em: w=  29, psites=   4, iter=   0 
em: w=  29, psites=   8, iter=   0 
em: w=  29, psites=  12, iter=   0 
em: w=  41, psites=   2, iter=   0 
em: w=  41, psites=   4, iter=   0 
em: w=  41, psites=   8, iter=   0 
em: w=  41, psites=  12, iter=   0 
em: w=  50, psites=   2, iter=   0 
em: w=  50, psites=   4, iter=   0 
em: w=  50, psites=   8, iter=   0 
em: w=  50, psites=  12, iter=   0 512  0.001275  0.007284  0.204865  0.002973  0.018715  0.005244  0.002324  0.012285  0.005033  0.019201  0.075522  0.012574  0.008996  0.005379  0.000431  0.001987 
 0.016522  0.001687  0.011552  0.068840  0.001795  0.799866  0.003121  0.002406  0.007124  0.002995  0.001674  0.043025  0.003281  0.004097  0.005937  0.013528  0.005584  0.003882  0.000962  0.002122






Time 235.36 secs.

P N
MOTIF 10 width = 18 sites = 9 llr = 305 E-value = 1.7e-021

NAME	START	P-VALUE				SITES
			Simplified	A	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	1	:	:
			pos.-specific	C	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
			probability	D	:	:	1	6	:	:	:	:	:	:	:	:	2	:	:	:	:	:
			matrix	E	:	:	4	1	:	:	:	:	:	:	:	:	:	:	:	2	:	:
				F	:	:	:	:	:	2	:	:	:	:	8	:	:	:	:	:	:	:
				G	:	:	:	1	2	1	7	:	:	8	:	:	:	:	:	:	:	:
				H	:	:	:	:	:	:	1	:	:	:	:	:	:	:	:	:	1	:
				I	:	:	:	:	:	:	:	:	:	:	:	:	:	2	:	:	:	7
				K	:	2	1	:	1	:	:	:	:	:	:	3	:	:	:	2	2	:
				L	:	:	:	:	:	1	:	1	1	:	2	:	:	2	a	2	:	1
				M	:	:	:	:	1	1	:	3	:	:	:	1	:	:	:	:	1	:
				N	:	:	1	:	2	:	1	:	:	:	:	1	:	:	:	1	:	:
				P	a	8	:	:	:	:	:	:	8	:	:	1	:	:	:	:	:	:
				Q	:	:	1	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				R	:	:	:	:	3	1	:	4	:	:	:	2	1	:	:	1	2	:
				S	:	:	:	2	:	:	:	:	:	2	:	:	:	:	:	:	2	:
				T	:	:	1	:	:	:	1	:	:	:	:	:	7	:	:	:	1	:
				V	:	:	:	:	:	:	:	1	1	:	:	1	:	6	:	:	:	2
				W	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:	:
				Y	:	:	:	:	:	3	:	:	:	:	:	:	:	:	:	:	:	:
.
			bits	6.3
				5.6
				5.0
				4.4
			Information	3.8
			content	3.1
			(49.0 bits)	2.5
				1.9
				1.3
				0.6
				0.0
.
			Multilevel		`P`	`P`	`E`	`D`	`R`	`Y`	`G`	`R`	`P`	`G`	`F`	`K`	`T`	`V`	`L`	`E`	`K`	`I`
			consensus			`K`		`S`	`G`	`F`		`M`		`S`	`L`	`R`	`D`	`I`		`K`	`R`	`V`
			sequence						`N`									`L`		`L`	`S`


.

A.thaliana	282	1.49e-18	`LKPLMGGTYF`		`P`	`P`	`N`	`D`	`N`	`Y`	`G`	`R`	`P`	`G`	`F`	`K`	`T`	`L`	`L`	`K`	`K`	`V`	`KDAWNSKRDT`
A.fulgidus	124	3.56e-18	`GKPFFGGTYF`		`P`	`P`	`E`	`D`	`R`	`Y`	`H`	`L`	`P`	`G`	`F`	`K`	`T`	`V`	`L`	`R`	`K`	`I`	`AEMWRHDRER`
D.melanogaster	198	6.00e-18	`LAPLVAGTYF`		`P`	`P`	`K`	`S`	`R`	`Y`	`G`	`M`	`P`	`S`	`F`	`N`	`T`	`V`	`L`	`K`	`S`	`I`	`ARKWETDKES`
C.elegans	139	9.80e-16	`LHPITGGTYF`		`P`	`P`	`D`	`D`	`N`	`R`	`G`	`M`	`L`	`G`	`F`	`P`	`T`	`I`	`L`	`N`	`M`	`I`	`HTEVVEKRRR`
M.thermoautotrophicum	128	8.69e-15	`GEPFFAGTYF`		`P`	`P`	`E`	`D`	`R`	`G`	`G`	`V`	`P`	`G`	`L`	`K`	`T`	`I`	`L`	`E`	`R`	`V`	`VMLWKKDADG`
D.radiodaurans	138	1.74e-14	`AEPFYAGTYF`		`P`	`P`	`Q`	`E`	`G`	`M`	`G`	`M`	`P`	`S`	`F`	`M`	`R`	`V`	`L`	`A`	`S`	`I`	`DDVWQNRRDQ`
H.sapiens	184	1.74e-14	`LQPFVGGTYF`		`P`	`P`	`E`	`D`	`G`	`L`	`T`	`R`	`V`	`G`	`F`	`R`	`T`	`V`	`L`	`L`	`R`	`I`	`REQWKQNKNT`
A.aeolicus	127	5.92e-13	`KEPFFAGTYI`		`P`	`K`	`E`	`G`	`M`	`F`	`G`	`R`	`P`	`G`	`L`	`R`	`D`	`L`	`L`	`L`	`T`	`I`	`RELWEKDRTK`
B.subtilis	129	1.09e-12	`QKPFYAGTYF`		`P`	`K`	`T`	`S`	`K`	`F`	`N`	`R`	`P`	`G`	`F`	`V`	`D`	`V`	`L`	`E`	`H`	`L`	`SETFANDREH`

Motif 10 block diagrams

Name

Lowest
p-value

Motifs

A.thaliana

1.5e-18

A.fulgidus

3.6e-18

D.melanogaster

6e-18

C.elegans

9.8e-16

M.thermoautotrophicum

8.7e-15

D.radiodaurans

1.7e-14

H.sapiens

1.7e-14

A.aeolicus

5.9e-13

B.subtilis

1.1e-12

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775	800	825	850

Motif 10 in BLOCKS format

BL   MOTIF 10 width=18 seqs=9
A.thaliana               (  282) PPNDNYGRPGFKTLLKKV  1 
A.fulgidus               (  124) PPEDRYHLPGFKTVLRKI  1 
D.melanogaster           (  198) PPKSRYGMPSFNTVLKSI  1 
C.elegans                (  139) PPDDNRGMLGFPTILNMI  1 
M.thermoautotrophicum    (  128) PPEDRGGVPGLKTILERV  1 
D.radiodaurans           (  138) PPQEGMGMPSFMRVLASI  1 
H.sapiens                (  184) PPEDGLTRVGFRTVLLRI  1 
A.aeolicus               (  127) PKEGMFGRPGLRDLLLTI  1 
B.subtilis               (  129) PKTSKFNRPGFVDVLEHL  1 
//

Motif 10 position-specific scoring matrix

log-odds matrix: alength= 20 w= 18 n= 7833 bayes= 9.89821 E= 1.7e-021 
  -311   -353   -425   -435   -475   -415   -404   -405   -365   -451   -425   -364    431   -323   -412   -307   -320   -403   -523   -508 
  -203   -268   -323   -319   -384   -334   -302   -298    111   -348   -315   -253    401   -206   -285   -199   -212   -296   -456   -421 
  -170   -284     78    217   -344   -247   -155   -252     97   -307   -209    153   -242    162   -155   -118     97   -242   -376   -281 
  -297   -323    327     26   -443     -2   -213   -384   -218   -459   -380     14   -350   -164   -318    112   -222   -385   -467   -368 
  -210   -266   -206   -158   -356    115   -143   -249    139   -299    172    240   -280    -22    217   -145   -135   -252   -351   -279 
  -180   -104   -269   -260    195    -91     13   -117   -208    -81     71   -165   -260   -183    -53   -150   -168   -148    -85    353 
  -240   -283   -212   -321   -449    342     49   -391   -267   -493   -374     74   -369   -271   -316   -197     -8   -383   -413   -399 
  -245   -157   -440   -378   -157   -379   -294     -9   -214     48    343   -266   -371   -221    248   -263   -171     98   -291   -254 
  -186   -247   -317   -313   -349   -325   -297   -232   -243    -83   -273   -251    400   -201   -297   -185   -196    -10   -440   -404 
  -213   -250   -294   -382   -461    351   -353   -398   -319   -504   -379   -181   -381   -328   -346     63   -286   -370   -420   -430 
  -377   -194   -475   -486    418   -478   -391   -149   -440    -12   -155   -377   -408   -402   -474   -329   -364   -236   -222    -85 
  -161   -226   -165   -113   -297   -241   -119   -198    234   -258    161    149     68     -2    154   -102    -93     44   -318   -239 
  -254   -202    119   -237   -381   -296   -244   -239   -172   -383   -239    -52   -334   -159     30    -41    373   -243   -410   -366 
  -301   -196   -550   -534   -282   -523   -496    256   -475     92   -151   -424   -486   -439   -506   -428   -241    313   -476   -421 
  -420   -294   -552   -515   -218   -513   -429    -99   -441    315    -74   -429   -444   -343   -430   -435   -341   -203   -386   -372 
    10   -215   -125    110   -278   -215   -101   -194    176     48   -150    150   -209     14     73    -73    -68   -192   -306   -219 
  -151   -224   -151   -101   -294   -231    145   -203    184   -258    160    -39   -226      5    152    141    101   -203   -315   -232 
  -326   -234   -423   -440   -259   -453   -426    408   -348    -24    -64   -305   -438   -339   -413   -329   -225    146   -393   -323

Motif 10 position-specific probability matrix

letter-probability matrix: alength= 20 w= 18 n= 7833 E= 1.7e-021 
 0.010639  0.001118  0.003190  0.003901  0.001649  0.004014  0.001737  0.002364  0.004233  0.004467  0.001263  0.002525  0.934589  0.003397  0.003412  0.007329  0.004946  0.003623  0.000471  0.001133 
 0.022619  0.002012  0.006485  0.008752  0.003110  0.007051  0.003512  0.004988  0.114317  0.009162  0.002713  0.005437  0.757579  0.007642  0.008187  0.015545  0.010437  0.007645  0.000748  0.002060 
 0.028343  0.001805  0.103984  0.359533  0.004096  0.012938  0.009764  0.006859  0.104137  0.012165  0.005658  0.090418  0.008837  0.097520  0.020161  0.027241  0.088668  0.011102  0.001304  0.005467 
 0.011720  0.001373  0.584717  0.095788  0.002066  0.070356  0.006517  0.002743  0.011722  0.004250  0.001727  0.034611  0.004180  0.010165  0.006543  0.133998  0.009724  0.004125  0.000694  0.002982 
 0.021461  0.002046  0.014522  0.026776  0.003763  0.158607  0.010626  0.007004  0.139278  0.012875  0.079219  0.165713  0.006792  0.027244  0.266386  0.022516  0.017769  0.010319  0.001548  0.005533 
 0.026371  0.006269  0.009429  0.013152  0.171887  0.037981  0.031280  0.017478  0.012544  0.058393  0.039471  0.010030  0.007772  0.008967  0.040972  0.021790  0.014183  0.021199  0.009755  0.441076 
 0.017450  0.001820  0.013988  0.008626  0.001982  0.766162  0.040007  0.002608  0.008334  0.003341  0.001805  0.052552  0.003649  0.004864  0.006629  0.015673  0.042909  0.004180  0.001006  0.002414 
 0.016894  0.004349  0.002871  0.005795  0.014948  0.005176  0.003712  0.036829  0.012031  0.142030  0.258938  0.004962  0.003594  0.006863  0.331372  0.009911  0.013888  0.116904  0.002341  0.006591 
 0.025360  0.002326  0.006765  0.009100  0.003949  0.007503  0.003653  0.007840  0.009876  0.057292  0.003631  0.005516  0.754404  0.007866  0.007557  0.017029  0.011672  0.055503  0.000835  0.002324 
 0.021076  0.002285  0.007934  0.005639  0.001822  0.815772  0.002465  0.002480  0.005820  0.003099  0.001738  0.008971  0.003359  0.003269  0.005390  0.095176  0.006222  0.004581  0.000960  0.001943 
 0.006768  0.003359  0.002259  0.002749  0.806206  0.002602  0.001893  0.013936  0.002523  0.093791  0.008219  0.002301  0.002797  0.001952  0.002208  0.006307  0.003638  0.011557  0.003773  0.021163 
 0.030136  0.002703  0.019317  0.036431  0.005656  0.013419  0.012493  0.009958  0.268230  0.017078  0.073619  0.087955  0.075378  0.031265  0.172577  0.030264  0.023808  0.080464  0.001943  0.007304 
 0.015887  0.003190  0.138634  0.015385  0.003169  0.009203  0.005268  0.007500  0.016120  0.007159  0.004585  0.021940  0.004660  0.010526  0.072661  0.046356  0.602716  0.010977  0.001029  0.003033 
 0.011465  0.003312  0.001345  0.001967  0.006299  0.001903  0.000920  0.230763  0.001977  0.193002  0.008443  0.001657  0.001622  0.001515  0.001778  0.003178  0.008516  0.517616  0.000652  0.002069 
 0.005013  0.001678  0.001325  0.002251  0.009800  0.002047  0.001455  0.019744  0.002492  0.904133  0.014382  0.001611  0.002169  0.002957  0.003002  0.003011  0.004269  0.014547  0.001217  0.002897 
 0.098448  0.002915  0.025436  0.170958  0.006455  0.016077  0.014181  0.010250  0.180407  0.142056  0.008516  0.088539  0.011093  0.035040  0.098115  0.037111  0.028218  0.015676  0.002115  0.008394 
 0.032329  0.002730  0.021378  0.039703  0.005798  0.014402  0.078179  0.009620  0.190261  0.017071  0.072801  0.023902  0.009857  0.032916  0.169692  0.163860  0.091354  0.014490  0.001989  0.007669 
 0.009609  0.002546  0.003240  0.003791  0.007379  0.003091  0.001488  0.665314  0.004748  0.086443  0.015401  0.003783  0.002265  0.003028  0.003378  0.006302  0.009534  0.163416  0.001159  0.004086






Time 256.80 secs.

P N
SUMMARY OF MOTIFS

Combined block diagrams: non-overlapping sites with p-value < 0.0001

Name

Combined
p-value

Motifs

A.thaliana

1.74e-262

C.elegans

4.44e-261

D.melanogaster

6.71e-270

H.sapiens

1.03e-282

A.aeolicus

6.98e-288

M.thermoautotrophicum

1.89e-262

B.subtilis

5.77e-285

D.radiodaurans

1.80e-251

M.tuberculosis

5.13e-212

A.fulgidus

7.10e-218

A.pernix

1.54e-191

Hthio

9.33e-01

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250	275	300	325	350	375	400	425	450	475	500	525	550	575	600	625	650	675	700	725	750	775	800	825	850

Stopped because nmotifs = 10 reached.


CPU: cfpub02.wi.mit.edu

EXPLANATION OF MEME RESULTS

The MEME results consist of:

The version of MEME and the date it was released.
The reference to cite if you use MEME in your research.
A description of the sequences you submitted (the "training set") showing the name, "weight" and length of each sequence.
The command line summary detailing the parameters with which you ran MEME.
Information on each of the motifs MEME discovered, including:
1. A summary line showing the width, number of occurrences, log likelihood ratio and statistical significance of the motif.
2. A simplified position-specific probability matrix.
3. A diagram showing the degree of conservation at each motif position.
4. A multilevel consensus sequence showing the most conserved letter(s) at each motif position.
5. The occurrences of the motif sorted by p-value and aligned with each other.
6. Block diagrams of the occurrences of the motif within each sequence in the training set.
7. The motif in BLOCKS or FASTA format.
8. A position-specific scoring matrix (PSSM) for use by the MAST database search program.
9. The position specific probability matrix (PSPM) describing the motif.
A summary of motifs showing an optimized (non-overlapping) tiling of all of the motifs onto each of the sequences in the training set.
The reason why MEME stopped and the name of the CPU on which it ran.
This explanation of how to interpret MEME results.

MOTIFS

For each motif that it discovers in the training set, MEME prints the following information:

Summary Line
This line gives the width (`width'), number of occurrences in the training set (`sites'), log likelihood ratio (`llr') and E-value of the motif. Each motif describes a pattern of a fixed width--no gaps are allowed in MEME motifs. MEME numbers the motifs consecutively from one as it finds them. MEME usually finds the most statistically significant (low E-value) motifs first. The statistical significance of a motif is based on its log likelihood ratio, its width and number of occurrences, the background letter frequencies (given in the command line summary), and the size of the training set. The E-value is an estimate of the expected number of motifs with the given log likelihood ratio (or higher), and with the same width and number of occurrences, that one would find in a similarly sized set of random sequences. (In random sequences each position is independent with letters chosen according to the background letter frequencies.) The log likelihood ratio is the logarithm of the ratio of the probability of the occurrences of the motif given the motif model (likelihood given the motif) versus their probability given the background model (likelihood given the null model). (Normally the background model is a 0-order Markov model using the background letter frequencies, but higher order Markov models may be specified via the -bfile option to MEME.) Clicking on the buttons to the left of the motif summary line takes you to the previous motif (P) or next motif (N).
Simplified Position-Specific Probability Matrix
MEME motifs are represented by position-specific probability matrices that specify the probability of each possible letter appearing at each possible position in an occurrence of the motif. In order to make it easier to see which letters are most likely in each of the columns of the motif, the simplified motif shows the letter probabilities multiplied by 10 rounded to the nearest integer. Zeros are replaced by ":" (the colon) for readability.

Information Content Diagram

The information content diagram provides an idea of which positions in the motif are most highly conserved. Each column (position) in a motif can be characterized by the amount of information it contains (measured in bits). Highly conserved positions in the motif have high information; positions where all letters are equally likely have low information. (The information content is relative to the background letter frequencies which are given in the command line summary section.) The diagram is printed so that each column lines up with the same column in the simplified position-specific probability matrix above it. Columns in the information content diagram are colored according to the majority category of the letters occurring in that column of the alignment. If no letter category has frequency above 0.5, the column in the diagram is colored black. For DNA sequences, the letter categories contain one letter each. For proteins, the categories are based on the biochemical properties of the various amino acids. The categories and their colors are:

NUCLEIC ACIDS	COLOR
A	RED
C	BLUE
G	ORANGE
T	GREEN

AMINO ACIDS	COLOR
ACFILVM	BLUE
NQST	GREEN
DE	MAGENTA
KR	RED
H	PINK
G	ORANGE
P	YELLOW
Y	TURQUOISE

Summing the information content for each position in the motif gives the total information content of the motif (shown in parentheses to the left of the diagram). The total information content is approximately equal to the log likelihood ratio divided by the number of occurrences times ln(2). The total information content gives a measure of the usefulness of the motif for database searches. For a motif to be useful for database searches, it must as a rule contain at least log_2(N) bits of information where N is the number of sequences in the database being searched. For example, to effectively search a database containing 100,000 sequences for occurrences of a single motif, the motif should have an IC of at least 16.6 bits. Motifs with lower information content are still useful when a family of sequences shares more than one motif since they can be combined in multiple motif searches (using MAST).

Multilevel Consensus Sequence
The multilevel consensus sequence corresponding to the motif is an aid in remembering and understanding the motif. It is calculated from the motif position-specific probability matrix as follows. Separately for each column of the motif, the letters in the alphabet are sorted in decreasing order by the probability with which they are expected to occur in that position of motif occurrences. The sorted letters are then printed vertically with the most probable letter on top. Only letters with probabilities of 0.2 or higher at that position in the motif are printed. As an example, the multilevel consensus sequence of motif 1 in the sample output is:
```
Multilevel TTATGTGAACGACGTCACACT
consensus  AA  T A G A GA     AA
sequence           T C TT     T
```
This multilevel consensus sequence says several things about the motif. First, the most likely form of the motif can be read from the top line as TTATGTGAACGACGTCACACT. Second, that only letter A has probability more than 0.2 in position 3 of the motif, both T and A have probability greater than 0.2 in position 1, etc. Third, a rough approximation of the motif can be made by converting the multilevel consensus sequence into the Prosite signature
Occurrences of the Motif
MEME displays the occurrences (sites) of the motif in the training set. The sites are shown aligned with each other, and the ten sequence positions preceding and following each site are also shown. Each site is identified by the name of the sequence where it occurs, the strand (if both strands of DNA sequences are being used), and the position in the sequence where the site begins. When the DNA strand is specified, `+' means the sequence in the training set, and `-' means the reverse complement of the training set sequence. (For `-' strands, the `start' position is actually the position on the positive strand where the site ends.) The sites are listed in order of increasing statistical significance (p-value). The p-value of a site is computed from the the match score of the site with the position specific scoring matrix for the motif. The p-value gives the probability of a random string (generated from the background letter frequencies) having the same match score or higher. (This is referred to as the position p-value by the MAST algorithm.)
Block Diagrams of Motif Occurrences
The occurrences of the motif in the training set sequences are shown with MAST-style block diagrams. One diagram is printed for each sequence showing all the occurrences of the motif in that sequence. The sequences are sorted by the lowest p-value among all occurrences of the motif in a given sequence. (The p-value of an occurrence is the probability of a single random subsequence the length of the motif, generated according to the 0-order background model, having a score at least as high as the score of the occurrence.) When the DNA strand is specified, `+' means the motif appears from left to right on the sequence, and `-' means the motif appears from right to left on the complementary strand. A sequence position scale is shown at the end of each table of block diagrams. Very long sequences are shown with thick lines connecting the motifs and are not drawn to scale.
Motif in BLOCKS format or FASTA format
For use with BLOCKS tools, MEME prints the occurrences of the motif in BLOCKS format.
You can convert these blocks to PSSMs (position-specific scoring matrices), LOGOS (color representations of the motifs), phylogeny trees and search them against a database of other blocks by pasting everything from the "BL" line to the "//" line (inclusive) into the Multiple Alignment Processor. If you include the -print_fasta switch on the command line, MEME prints the motif sites in FASTA format instead of BLOCKS format.
Position-Specific Scoring Matrix
The position-specific scoring matrix corresponding to the motif is printed for use by database search programs such as MAST. This matrix is a log-odds matrix calculated by taking the log (base 2) of the ratio p/f at each position in the motif where p is the probability of a particular letter at that position in the motif, and f is the background frequency of the letter (given in the command line summary section.) This is the same matrix that is used above in computing the p-values of the occurrences of the motif in the Occurrences of the Motif and Block Diagrams of Motif Occurrences sections. The scoring matrix is printed "sideways"--columns correspond to the letters in the alphabet (in the same order as shown in the simplified motif) and rows corresponding to the positions of the motif, position one first. The scoring matrix is preceded by a line starting with "log-odds matrix:" and containing the length of the alphabet, width of the motif, number of characters in the training set and the scoring threshold used in the list of possible motif examples.
Position-Specific Probability Matrix
The motif itself is a position-specific probability matrix giving, for each position in the pattern, the probabilities of each possible letter occurring there. The probability matrix is printed "sideways"--columns correspond to the letters in the alphabet (in the same order as shown in the simplified motif) and rows corresponding to the positions of the motif, position one first. The motif is preceded by a line starting with "letter-probability matrix:" and containing the length of the alphabet, width of the motif and number of characters in the training set.

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P N MOTIF 1 width = 50 sites = 11 llr = 1400 E-value = 7.7e-351

P N MOTIF 2 width = 50 sites = 11 llr = 1281 E-value = 1.4e-285

P N MOTIF 3 width = 50 sites = 11 llr = 1195 E-value = 2.0e-246

P N MOTIF 4 width = 41 sites = 11 llr = 809 E-value = 3.8e-107

P N MOTIF 5 width = 42 sites = 11 llr = 794 E-value = 1.4e-090

P N MOTIF 6 width = 27 sites = 11 llr = 560 E-value = 1.8e-075

P N MOTIF 7 width = 28 sites = 8 llr = 436 E-value = 3.5e-038

P N MOTIF 8 width = 23 sites = 10 llr = 412 E-value = 3.8e-038

P N MOTIF 9 width = 21 sites = 11 llr = 410 E-value = 3.7e-037

P N MOTIF 10 width = 18 sites = 9 llr = 305 E-value = 1.7e-021

P NSUMMARY OF MOTIFS

Combined block diagrams: non-overlapping sites with p-value < 0.0001

Stopped because nmotifs = 10 reached.

EXPLANATION OF MEME RESULTS

The MEME results consist of:

Summary Line

Simplified Position-Specific Probability Matrix

Information Content Diagram

Multilevel Consensus Sequence

Occurrences of the Motif

Block Diagrams of Motif Occurrences

Motif in BLOCKS format or FASTA format

Position-Specific Scoring Matrix

Position-Specific Probability Matrix

P N
MOTIF 1 width = 50 sites = 11 llr = 1400 E-value = 7.7e-351

P N
MOTIF 2 width = 50 sites = 11 llr = 1281 E-value = 1.4e-285

P N
MOTIF 3 width = 50 sites = 11 llr = 1195 E-value = 2.0e-246

P N
MOTIF 4 width = 41 sites = 11 llr = 809 E-value = 3.8e-107

P N
MOTIF 5 width = 42 sites = 11 llr = 794 E-value = 1.4e-090

P N
MOTIF 6 width = 27 sites = 11 llr = 560 E-value = 1.8e-075

P N
MOTIF 7 width = 28 sites = 8 llr = 436 E-value = 3.5e-038

P N
MOTIF 8 width = 23 sites = 10 llr = 412 E-value = 3.8e-038

P N
MOTIF 9 width = 21 sites = 11 llr = 410 E-value = 3.7e-037

P N
MOTIF 10 width = 18 sites = 9 llr = 305 E-value = 1.7e-021

P N
SUMMARY OF MOTIFS