MEME

MEME - Motif discovery tool

MEME version 3.0 (Release date: 2004/07/26 08:17:15)

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= GCN4_YPD.fsa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
iYJR109C                 1.0000    688  iYDR126W                 1.0000    246  
iYHR018C                 1.0000    500  iYER052C                 1.0000    787  
iYOL141W                 1.0000    224  iYJL089W                 1.0000    102  
iYOL059W                 1.0000    784  iYER055C                 1.0000    753  
iYMR062C                 1.0000    711  iYLR355C                 1.0000   1056  
iYKL016C                 1.0000    576  iYEL063C                 1.0000    940  
iYOR336W                 1.0000    482  iYER068W                 1.0000    597  
iYOR107W                 1.0000    757  iYCL030C                 1.0000    290  
iYHR070W                 1.0000    544  iYDL198C                 1.0000    354  
iYDL171C                 1.0000    700  iYNL005C                 1.0000    924  
iYDR481C                 1.0000    184  iYGL184C                 1.0000    527  
iYOL064C                 1.0000    218  iYOR301W                 1.0000    467  
iYOR130C                 1.0000   1161  iYBR115C                 1.0000    238  
iYJL200C                 1.0000    302  iYLL005C                 1.0000    543  
itT(AGU)J                1.0000    335  iYBR043C                 1.0000    398  
iYDR084C                 1.0000    265  iYOL154W                 1.0000   1421  
iYDR235W                 1.0000    109  iYBR249C                 1.0000   1066  
iYPR110C                 1.0000    481  iYER072W                 1.0000    843  
iYHR161C                 1.0000    775  iYBR113W                 1.0000   1212  
iYJL072C                 1.0000    258  iYBL076C                 1.0000    211  
iYOL119C                 1.0000    260  iYJR111C                 1.0000    340  
iYGR267C                 1.0000    327  iYGR271W                 1.0000    360  
iYJLWdelta9              1.0000    525  iYER089C                 1.0000    619  
iYNL104C                 1.0000    999  iYJR016C                 1.0000    311  
iYOR221C                 1.0000    506  iYPL274W                 1.0000    390  
iYEL062W                 1.0000    288  iYBR248C                 1.0000    363  
iYDR341C                 1.0000    592  iYNR050C                 1.0000   1361  
iYDR125C                 1.0000    478  iYBR144C                 1.0000    227  
itM(CAU)P                1.0000   1037  iYDR034C                 1.0000    888  
iYGL126W                 1.0000    399

COMMAND LINE SUMMARY

This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme GCN4_YPD.fsa -dna -nmotifs 5 -minw 7 -maxw 11 -revcomp 

model:  mod=         zoops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            7    maxw=           11    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=       59    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=           33299    N=              59
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.322 C 0.178 G 0.178 T 0.322 
Background letter frequencies (from dataset with add-one prior applied):
A 0.322 C 0.178 G 0.178 T 0.322

MOTIF 1 width = 11 sites = 59 llr = 515 E-value = 1.7e-020

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	:	:	:	1	:	:	1	:	2	:
				pos.-specific	C	2	:	2	:	:	3	1	:	4	:	6
				probability	G	:	:	:	:	:	:	:	:	:	1	:
				matrix	T	8	a	8	a	9	6	9	9	6	8	4
.
				bits	2.5
					2.2
					2.0
					1.7
				Information	1.5
				content	1.2
				(12.6 bits)	1.0
					0.7
					0.5
					0.2
					0.0
.
				Multilevel		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`
				consensus							`C`			`C`		`T`
				sequence

.
iYNR050C	+	1295	5.12e-06	`GTTTTATGAT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`TTTTTCAAAT`
iYOR221C	+	275	5.12e-06	`CTCTGGAACT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`AGTTTTTTCG`
iYJR016C	+	229	5.12e-06	`TAGTTAATTT`		`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`T`	`T`	`C`	`ATGGGTTCAG`
iYER089C	-	119	5.12e-06	`TACTTTCTCT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`ATTGATTAAT`
iYGR267C	+	258	5.12e-06	`TGTTCGGTCT`		`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`T`	`T`	`C`	`GGTGAGCGAC`
iYJL072C	-	126	5.12e-06	`ATGACTAACC`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`C`	`CAGCGTGAAA`
iYBR113W	+	1030	5.12e-06	`TTCCCTTTTC`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`AAGTTTCGGA`
iYER072W	+	545	5.12e-06	`ATTCTCTTTC`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`ACAAACTGAG`
iYJL200C	-	241	5.12e-06	`TTTTTTTTTT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`ACGCTCTTGA`
iYOR301W	+	353	5.12e-06	`TTTTTTTTTT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`TTCAGAACTA`
iYOR107W	-	533	5.12e-06	`TTTTTTTTTT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`ATTTTTTGGC`
iYER068W	+	434	5.12e-06	`ACTCTTCTAT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`ATATAAAGAG`
iYOR336W	+	284	5.12e-06	`TTTTTTTTTT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`GAGCAGATTG`
iYER055C	+	478	5.12e-06	`CATTCTTACT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`TTTTTGGCTT`
iYER052C	-	234	5.12e-06	`TCATCACTTT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`ACTTTCCGTA`
iYHR018C	+	141	5.12e-06	`TAATCCTTTT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`ACATGTTTCA`
iYGL126W	-	230	1.72e-05	`GAAATATCAC`		`C`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`TACTTTTCGT`
iYDR034C	+	865	1.72e-05	`TATTATAATT`		`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`C`	`T`	`T`	`TTCCTTTTCA`
iYDR341C	+	153	1.72e-05	`ATGAAAGTAA`		`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`C`	`T`	`T`	`TTAAGTGACG`
iYEL062W	+	32	1.72e-05	`CATCAAAATG`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`TTTTAATATT`
iYNL104C	+	64	1.72e-05	`GTGAGAATCC`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`CAAAAAATAC`
iYJR111C	-	299	1.72e-05	`TACTCTAATT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`GTTTATTGGC`
iYBL076C	-	130	1.72e-05	`CGAAAAATTT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`GTTTCCGCAG`
iYHR161C	-	514	1.72e-05	`AACGCTTTTC`		`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`C`	`T`	`T`	`TTTTTTTCCA`
iYBR249C	+	834	1.72e-05	`AGCCTTTGTT`		`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`T`	`T`	`T`	`CTTTCTATTT`
iYDL198C	+	206	1.72e-05	`TTTTCATTTT`		`C`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`GGGCAGTGGC`
iYEL063C	+	25	1.72e-05	`TTGCTATGCC`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`TTGTTTTTAC`
iYJR109C	-	188	1.72e-05	`AAAATCCAAT`		`C`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`CGTCATAAGC`
iYOL154W	+	237	2.00e-05	`AACAATAGCA`		`T`	`T`	`C`	`T`	`T`	`C`	`T`	`T`	`C`	`T`	`C`	`AATTTTACAA`
iYPL274W	-	176	2.51e-05	`GTACTTTTCA`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`A`	`C`	`TCCAGAATGC`
iYOL141W	-	122	2.51e-05	`ATGTTGCAAT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`A`	`C`	`GCTTTTAAAT`
iYDR126W	+	29	2.51e-05	`GAACATGAAA`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`A`	`C`	`TCGGTTTTTT`
iYPR110C	+	62	3.98e-05	`ATGAGTGAAA`		`T`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`T`	`C`	`AACTCATCGC`
iYLL005C	-	460	3.98e-05	`TTTGTCACTT`		`T`	`T`	`C`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`CAAATTACGG`
iYDL171C	+	414	3.98e-05	`AATTTATTGC`		`T`	`T`	`C`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`ACGTTTTGCG`
iYHR070W	-	140	3.98e-05	`TCCTAATTTA`		`T`	`T`	`C`	`T`	`T`	`C`	`T`	`T`	`C`	`T`	`T`	`TATATAACAG`
iYDR125C	+	190	4.77e-05	`TGGTCTGAAT`		`T`	`T`	`T`	`T`	`A`	`T`	`T`	`T`	`T`	`T`	`C`	`AAAAATGAGG`
iYBR248C	+	209	4.77e-05	`TATGACTCAA`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`G`	`C`	`AGAAGAGTAA`
iYLR355C	+	204	4.77e-05	`GATTAATTAT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`G`	`C`	`GTCCTACAGC`
iYBR115C	+	57	5.98e-05	`TAAACTCAGA`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`A`	`T`	`ACTATTGGCT`
iYNL005C	-	549	5.98e-05	`ATTTTACAAA`		`C`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`C`	`A`	`C`	`CTCCCTTATC`
iYCL030C	-	15	6.77e-05	`GTTTACAAAA`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`G`	`AATAATGGTT`
iYGR271W	+	102	7.29e-05	`GCATTTAGAA`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`A`	`C`	`T`	`C`	`AAAAAAGTCA`
iYOL059W	+	135	8.42e-05	`ATTTTCTATT`		`C`	`T`	`C`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`TAAGAATCTA`
iYOR130C	+	1092	1.05e-04	`TGCAACATTT`		`T`	`T`	`T`	`T`	`A`	`T`	`T`	`T`	`T`	`T`	`T`	`CAAATCATAT`
iYDR481C	+	125	1.05e-04	`ACTAAAATCC`		`C`	`T`	`T`	`T`	`A`	`C`	`T`	`T`	`T`	`T`	`C`	`CTCTACGCGC`
iYKL016C	+	193	1.05e-04	`TTGGTGTATC`		`T`	`T`	`T`	`T`	`A`	`C`	`T`	`T`	`T`	`T`	`T`	`TGGGGGCATC`
iYOL064C	+	101	1.09e-04	`GTGGCATGGT`		`T`	`T`	`C`	`T`	`T`	`C`	`T`	`T`	`T`	`G`	`C`	`AAACTGAAAG`
iYOL119C	+	108	1.12e-04	`CCAAGGAATA`		`T`	`T`	`T`	`T`	`C`	`C`	`T`	`T`	`C`	`T`	`C`	`TGAAATAGGC`
itM(CAU)P	+	935	1.20e-04	`TCTAAGACTG`		`T`	`T`	`T`	`C`	`T`	`C`	`T`	`T`	`C`	`T`	`C`	`TTGGTCTGTA`
iYMR062C	+	496	1.20e-04	`CAAAACATGA`		`C`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`T`	`A`	`T`	`CACTAAAAGT`
iYGL184C	+	41	1.70e-04	`TGCTTGATAT`		`T`	`T`	`T`	`T`	`T`	`G`	`T`	`T`	`T`	`T`	`T`	`AATGAACTGT`
iYDR235W	-	70	3.28e-04	`AGGCTAGTAG`		`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`A`	`A`	`C`	`GGTCATTAAG`
iYBR043C	-	298	3.45e-04	`CTTTTATCAC`		`T`	`T`	`T`	`T`	`A`	`C`	`C`	`T`	`C`	`T`	`T`	`CGTAAATATC`
itT(AGU)J	+	1	4.40e-04			`T`	`T`	`C`	`T`	`A`	`T`	`T`	`T`	`T`	`A`	`T`	`ATTTGCCTGA`
iYDR084C	+	67	6.09e-04	`AAGAACCACG`		`C`	`T`	`T`	`T`	`T`	`C`	`T`	`A`	`C`	`A`	`T`	`TTACATTATG`
iYJLWdelta9	-	466	7.59e-04	`ATTATGCAAT`		`A`	`T`	`T`	`T`	`T`	`C`	`C`	`T`	`C`	`T`	`T`	`AATAAAAAAC`
iYJL089W	+	45	7.59e-04	`ACTCATTCAG`		`C`	`T`	`C`	`T`	`T`	`C`	`C`	`T`	`C`	`T`	`G`	`ATAGCAGTGA`
iYBR144C	-	101	9.31e-04	`CTTGTAGTCC`		`C`	`T`	`C`	`T`	`T`	`T`	`T`	`A`	`T`	`A`	`T`	`TCGTAGTATG`

Motif 1 block diagrams

Name

Lowest
p-value

Motifs

iYNR050C

5.1e-06

iYOR221C

5.1e-06

iYJR016C

5.1e-06

iYER089C

5.1e-06

-1

iYGR267C

5.1e-06

iYJL072C

5.1e-06

-1

iYBR113W

5.1e-06

iYER072W

5.1e-06

iYJL200C

5.1e-06

-1

iYOR301W

5.1e-06

iYOR107W

5.1e-06

-1

iYER068W

5.1e-06

iYOR336W

5.1e-06

iYER055C

5.1e-06

iYER052C

5.1e-06

-1

iYHR018C

5.1e-06

iYGL126W

1.7e-05

-1

iYDR034C

1.7e-05

iYDR341C

1.7e-05

iYEL062W

1.7e-05

iYNL104C

1.7e-05

iYJR111C

1.7e-05

-1

iYBL076C

1.7e-05

-1

iYHR161C

1.7e-05

-1

iYBR249C

1.7e-05

iYDL198C

1.7e-05

iYEL063C

1.7e-05

iYJR109C

1.7e-05

-1

iYOL154W

2e-05

iYPL274W

2.5e-05

-1

iYOL141W

2.5e-05

-1

iYDR126W

2.5e-05

iYPR110C

4e-05

iYLL005C

4e-05

-1

iYDL171C

4e-05

iYHR070W

4e-05

-1

iYDR125C

4.8e-05

iYBR248C

4.8e-05

iYLR355C

4.8e-05

iYBR115C

6e-05

iYNL005C

6e-05

-1

iYCL030C

6.8e-05

-1

iYGR271W

7.3e-05

iYOL059W

8.4e-05

iYOR130C

0.0001

iYDR481C

0.0001

iYKL016C

0.0001

iYOL064C

0.00011

iYOL119C

0.00011

itM(CAU)P

0.00012

iYMR062C

0.00012

iYGL184C

0.00017

iYDR235W

0.00033

-1

iYBR043C

0.00035

-1

itT(AGU)J

0.00044

iYDR084C

0.00061

iYJLWdelta9

0.00076

-1

iYJL089W

0.00076

iYBR144C

0.00093

-1

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	875	900	925	950	975

Motif 1 in BLOCKS format

BL   MOTIF 1 width=11 seqs=59
iYNR050C                 ( 1295) TTTTTTTTTTC  1 
iYOR221C                 (  275) TTTTTTTTTTC  1 
iYJR016C                 (  229) TTTTTCTTTTC  1 
iYER089C                 (  119) TTTTTTTTTTC  1 
iYGR267C                 (  258) TTTTTCTTTTC  1 
iYJL072C                 (  126) TTTTTTTTCTC  1 
iYBR113W                 ( 1030) TTTTTTTTTTC  1 
iYER072W                 (  545) TTTTTTTTTTC  1 
iYJL200C                 (  241) TTTTTTTTTTC  1 
iYOR301W                 (  353) TTTTTTTTTTC  1 
iYOR107W                 (  533) TTTTTTTTTTC  1 
iYER068W                 (  434) TTTTTTTTTTC  1 
iYOR336W                 (  284) TTTTTTTTTTC  1 
iYER055C                 (  478) TTTTTTTTTTC  1 
iYER052C                 (  234) TTTTTTTTTTC  1 
iYHR018C                 (  141) TTTTTTTTTTC  1 
iYGL126W                 (  230) CTTTTTTTTTC  1 
iYDR034C                 (  865) TTTTTCTTCTT  1 
iYDR341C                 (  153) TTTTTCTTCTT  1 
iYEL062W                 (   32) TTTTTTTTTTT  1 
iYNL104C                 (   64) TTTTTTTTCTT  1 
iYJR111C                 (  299) TTTTTTTTTTT  1 
iYBL076C                 (  130) TTTTTTTTTTT  1 
iYHR161C                 (  514) TTTTTCTTCTT  1 
iYBR249C                 (  834) TTTTTCTTTTT  1 
iYDL198C                 (  206) CTTTTTTTTTC  1 
iYEL063C                 (   25) TTTTTTTTTTT  1 
iYJR109C                 (  188) CTTTTTTTTTC  1 
iYOL154W                 (  237) TTCTTCTTCTC  1 
iYPL274W                 (  176) TTTTTTTTCAC  1 
iYOL141W                 (  122) TTTTTTTTCAC  1 
iYDR126W                 (   29) TTTTTTTTCAC  1 
iYPR110C                 (   62) TTTTTTCTTTC  1 
iYLL005C                 (  460) TTCTTTTTCTT  1 
iYDL171C                 (  414) TTCTTTTTTTT  1 
iYHR070W                 (  140) TTCTTCTTCTT  1 
iYDR125C                 (  190) TTTTATTTTTC  1 
iYBR248C                 (  209) TTTTTTTTTGC  1 
iYLR355C                 (  204) TTTTTTTTTGC  1 
iYBR115C                 (   57) TTTTTTTTTAT  1 
iYNL005C                 (  549) CTTTTCTTCAC  1 
iYCL030C                 (   15) TTTTTTTTCTG  1 
iYGR271W                 (  102) TTTTTTTACTC  1 
iYOL059W                 (  135) CTCTTTTTCTT  1 
iYOR130C                 ( 1092) TTTTATTTTTT  1 
iYDR481C                 (  125) CTTTACTTTTC  1 
iYKL016C                 (  193) TTTTACTTTTT  1 
iYOL064C                 (  101) TTCTTCTTTGC  1 
iYOL119C                 (  108) TTTTCCTTCTC  1 
itM(CAU)P                (  935) TTTCTCTTCTC  1 
iYMR062C                 (  496) CTTTTCTTTAT  1 
iYGL184C                 (   41) TTTTTGTTTTT  1 
iYDR235W                 (   70) TTTTTCTTAAC  1 
iYBR043C                 (  298) TTTTACCTCTT  1 
itT(AGU)J                (    1) TTCTATTTTAT  1 
iYDR084C                 (   67) CTTTTCTACAT  1 
iYJLWdelta9              (  466) ATTTTCCTCTT  1 
iYJL089W                 (   45) CTCTTCCTCTG  1 
iYBR144C                 (  101) CTCTTTTATAT  1 
//

Motif 1 position-specific scoring matrix

log-odds matrix: alength= 4 w= 11 n= 32709 bayes= 10.3757 E= 1.7e-020 
  -424     -7  -1253    134 
 -1253  -1253  -1253    164 
 -1253    -22  -1253    140 
 -1253   -339  -1253    161 
  -166   -339  -1253    145 
 -1253     93   -339    100 
 -1253   -139  -1253    153 
  -266  -1253  -1253    156 
  -424    100  -1253     96 
   -92  -1253   -181    128 
 -1253    169   -239     28

Motif 1 position-specific probability matrix

letter-probability matrix: alength= 4 w= 11 nsites= 59 E= 1.7e-020 
 0.016949  0.169492  0.000000  0.813559 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.152542  0.000000  0.847458 
 0.000000  0.016949  0.000000  0.983051 
 0.101695  0.016949  0.000000  0.881356 
 0.000000  0.338983  0.016949  0.644068 
 0.000000  0.067797  0.000000  0.932203 
 0.050847  0.000000  0.000000  0.949153 
 0.016949  0.355932  0.000000  0.627119 
 0.169492  0.000000  0.050847  0.779661 
 0.000000  0.576271  0.033898  0.389831






Time 159.41 secs.

MOTIF 2 width = 11 sites = 58 llr = 497 E-value = 1.1e-014

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	2	4	2	:	:	9	:	:	2	9	:
				pos.-specific	C	2	1	3	:	:	:	4	:	8	:	3
				probability	G	4	3	3	:	a	:	6	:	:	:	:
				matrix	T	2	2	1	9	:	1	:	a	:	1	7
.
				bits	2.5
					2.2
					2.0
					1.7
				Information	1.5
				content	1.2
				(12.4 bits)	1.0
					0.7
					0.5
					0.2
					0.0
.
				Multilevel		`G`	`A`	`C`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`
				consensus		`T`	`G`	`G`				`C`				`C`
				sequence		`A`		`A`

.
iYEL063C	-	363	2.21e-07	`TGTGGTTTCC`		`G`	`G`	`G`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`ACGGCTTTTT`
iYER068W	-	375	4.21e-07	`TTTTGATGTA`		`G`	`A`	`C`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`TCGGATAAGA`
iYBR113W	-	487	7.93e-07	`CACCCGGATT`		`G`	`G`	`C`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`C`	`CTTCATCGCG`
iYHR161C	+	407	7.93e-07	`ACAAAAGCCA`		`G`	`G`	`C`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`C`	`GTCAGTTGCT`
iYGL184C	-	386	7.93e-07	`TTGGTTATCC`		`G`	`G`	`C`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`T`	`TCTGACTCTT`
iYOL064C	+	148	2.77e-06	`GATATTGCTC`		`G`	`T`	`C`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`TCGCGCATTT`
iYDL171C	+	571	2.77e-06	`GGCTACCAGG`		`G`	`T`	`C`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`CAAAGAAAAA`
iYOR221C	-	341	3.74e-06	`ATCGCGACTG`		`C`	`A`	`C`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`CAACAACAAG`
iYDR126W	-	7	3.74e-06	`TTCATGTTCG`		`G`	`G`	`A`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`ATGCAT`
iYJR109C	+	345	3.74e-06	`AGACAGTGGT`		`G`	`G`	`A`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`TTTCTCAACC`
iYJR016C	+	130	4.85e-06	`ACTACTATAT`		`T`	`A`	`C`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`CTGGAGAGGA`
iYGR267C	-	47	4.85e-06	`GATTGTGCGT`		`G`	`C`	`G`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`T`	`TTTTTGTTAG`
iYMR062C	+	148	4.85e-06	`ACGAATTACG`		`C`	`A`	`G`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`CCTACCTGTC`
iYER089C	+	451	6.56e-06	`CACAGTGATT`		`T`	`G`	`C`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`T`	`TACGATTTTT`
iYBR043C	-	346	6.56e-06	`TAAATAGTCA`		`G`	`A`	`A`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`TGTAAATAGA`
iYER052C	+	289	6.56e-06	`AAGAAAGAAA`		`A`	`G`	`G`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`GGGCCTGAAA`
iYNL005C	+	612	8.22e-06	`CATCAACGAA`		`T`	`G`	`G`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`C`	`CATTTAATGC`
iYLR355C	+	298	8.22e-06	`TACGAAACGC`		`G`	`G`	`A`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`C`	`TGACAGCCAC`
iYHR018C	+	183	1.01e-05	`CTTATCCAAA`		`A`	`A`	`G`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`TCATCTACTA`
iYOR130C	+	227	1.18e-05	`TTCGAGCTCA`		`A`	`G`	`G`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`C`	`GATGCAGAAC`
iYOR107W	+	489	1.18e-05	`CGGTCGTAGT`		`G`	`A`	`A`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`T`	`ATTTTTCCAT`
iYOL059W	+	422	1.18e-05	`TGTGATTTTT`		`T`	`A`	`G`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`T`	`GTCGCATTTG`
iYDR341C	+	195	1.33e-05	`AGAAAGAAAT`		`A`	`A`	`C`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`T`	`TAGACACTTT`
iYNL104C	+	95	1.33e-05	`CCTTTGAAAG`		`A`	`A`	`C`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`C`	`TTACACGTAA`
iYKL016C	+	331	1.33e-05	`TCGTTTATGG`		`G`	`A`	`T`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`CGGATATGTC`
iYGL126W	-	1	1.49e-05	`CGCCAACTTT`		`T`	`C`	`C`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`
iYDL198C	+	137	1.49e-05	`AGCAAATGCA`		`C`	`A`	`G`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`C`	`GAGTTTTTGT`
iYCL030C	-	202	1.49e-05	`AACCCATGCA`		`C`	`A`	`G`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`C`	`GTTTTTTTAT`
iYER055C	-	192	1.49e-05	`AAAAGCTTCC`		`A`	`A`	`G`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`C`	`CTCTACCGTT`
iYOL141W	-	43	1.49e-05	`CATGTACTTT`		`A`	`A`	`G`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`C`	`ATAGCGAGCT`
itM(CAU)P	+	580	1.79e-05	`CGGGTGCAAT`		`C`	`C`	`C`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`T`	`CAATGTTTAT`
iYJL089W	+	82	2.20e-05	`GAGGGTCACG`		`T`	`C`	`G`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`T`	`ATGCTTTCTT`
iYER072W	+	599	2.57e-05	`GTTGGAAGAC`		`T`	`T`	`C`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`T`	`CACTACGCAG`
iYOR336W	-	206	2.57e-05	`TCAAAGAATC`		`T`	`A`	`A`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`GGGGAGCACG`
iYOL119C	+	198	2.87e-05	`TCATAGGCAC`		`G`	`G`	`C`	`T`	`G`	`A`	`C`	`T`	`A`	`A`	`T`	`TTGAAGCTAT`
iYBR249C	+	318	2.87e-05	`TTCATTTCAT`		`C`	`G`	`T`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`TTCGCAGTAA`
iYOR301W	+	131	4.24e-05	`GTGGAAGGGT`		`G`	`T`	`T`	`T`	`G`	`A`	`C`	`T`	`C`	`A`	`T`	`CATCGCATCG`
iYBR115C	+	165	4.57e-05	`GGTATTTCGA`		`C`	`A`	`T`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`C`	`ACGCGAAAAA`
iYDR034C	+	247	5.76e-05	`CATTTCTTCC`		`A`	`A`	`T`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`C`	`GTCGCGTCCT`
iYJL200C	-	226	6.28e-05	`TTTTTCACGC`		`T`	`C`	`T`	`T`	`G`	`A`	`G`	`T`	`C`	`A`	`T`	`CGCGAGTAAA`
iYJR111C	-	160	7.57e-05	`CTAAAAAAAT`		`G`	`T`	`G`	`T`	`G`	`A`	`C`	`T`	`A`	`A`	`T`	`AATTACTCAA`
iYBR248C	+	112	1.24e-04	`ATGTTTCGAT`		`G`	`T`	`C`	`T`	`G`	`A`	`C`	`T`	`C`	`T`	`T`	`TTCTCATGAA`
iYNR050C	+	211	1.33e-04	`CGATTCCAGA`		`G`	`T`	`A`	`T`	`G`	`A`	`G`	`T`	`A`	`A`	`T`	`TCTTTTCACT`
iYBR144C	+	147	1.44e-04	`ACTACTGCTT`		`T`	`A`	`C`	`T`	`G`	`T`	`C`	`T`	`C`	`A`	`C`	`AATGTCTCTG`
iYPR110C	+	245	1.57e-04	`TAAGCATGTC`		`T`	`T`	`C`	`T`	`G`	`A`	`C`	`T`	`A`	`A`	`T`	`TTTTATATAC`
iYOL154W	-	897	1.99e-04	`AAATATTGTT`		`C`	`A`	`C`	`T`	`G`	`A`	`C`	`T`	`G`	`A`	`C`	`AAATCTAAAA`
iYJL072C	-	138	2.14e-04	`GGAAGATCAG`		`T`	`G`	`A`	`T`	`G`	`A`	`C`	`T`	`A`	`A`	`C`	`CTTTTTTTTC`
iYPL274W	-	237	2.30e-04	`CTGATATCAA`		`A`	`A`	`A`	`T`	`G`	`A`	`C`	`T`	`A`	`A`	`T`	`ACTCTGCAAA`
iYHR070W	+	38	2.46e-04	`AAAAGAAACG`		`A`	`G`	`A`	`T`	`G`	`A`	`C`	`T`	`A`	`A`	`C`	`ACCTTTATCT`
iYGR271W	-	1	2.80e-04	`GTTGTTTTAA`		`T`	`T`	`G`	`T`	`G`	`T`	`C`	`T`	`C`	`A`	`C`
iYBL076C	-	87	2.80e-04	`CTCGAAACAA`		`T`	`G`	`A`	`T`	`G`	`A`	`C`	`T`	`C`	`T`	`T`	`AAGCATGAAA`
iYLL005C	+	108	5.03e-04	`ACACGCTATA`		`A`	`T`	`T`	`T`	`G`	`T`	`G`	`T`	`C`	`A`	`T`	`AAAGAATTTT`
iYEL062W	+	201	5.28e-04	`TCTAATGAAT`		`A`	`A`	`C`	`T`	`G`	`A`	`G`	`T`	`A`	`T`	`T`	`CTTTACATAC`
itT(AGU)J	+	84	5.53e-04	`TGATGTTGAT`		`G`	`T`	`G`	`A`	`G`	`A`	`G`	`T`	`A`	`A`	`T`	`AAGCACTGTG`
iYDR235W	-	92	5.79e-04	`GAGATCT`		`G`	`C`	`G`	`G`	`G`	`A`	`G`	`T`	`G`	`A`	`T`	`GAGGCTAGTA`
iYJLWdelta9	+	224	6.08e-04	`TTACAAGCTT`		`C`	`C`	`G`	`T`	`A`	`A`	`C`	`T`	`C`	`A`	`T`	`ACAGACTTCT`
iYDR125C	+	372	8.15e-04	`TATCAACAAA`		`G`	`G`	`T`	`A`	`G`	`T`	`G`	`T`	`C`	`A`	`T`	`TGTATATATA`
iYDR084C	-	229	8.15e-04	`TTTTGCAATA`		`G`	`A`	`A`	`G`	`G`	`C`	`G`	`T`	`C`	`A`	`T`	`ACATATTTAT`

Motif 2 block diagrams

Name

Lowest
p-value

Motifs

iYEL063C

2.2e-07

-2

iYER068W

4.2e-07

-2

iYBR113W

7.9e-07

-2

iYHR161C

7.9e-07

iYGL184C

7.9e-07

-2

iYOL064C

2.8e-06

iYDL171C

2.8e-06

iYOR221C

3.7e-06

-2

iYDR126W

3.7e-06

-2

iYJR109C

3.7e-06

iYJR016C

4.8e-06

iYGR267C

4.8e-06

-2

iYMR062C

4.8e-06

iYER089C

6.6e-06

iYBR043C

6.6e-06

-2

iYER052C

6.6e-06

iYNL005C

8.2e-06

iYLR355C

8.2e-06

iYHR018C

1e-05

iYOR130C

1.2e-05

iYOR107W

1.2e-05

iYOL059W

1.2e-05

iYDR341C

1.3e-05

iYNL104C

1.3e-05

iYKL016C

1.3e-05

iYGL126W

1.5e-05

-2

iYDL198C

1.5e-05

iYCL030C

1.5e-05

-2

iYER055C

1.5e-05

-2

iYOL141W

1.5e-05

-2

itM(CAU)P

1.8e-05

iYJL089W

2.2e-05

iYER072W

2.6e-05

iYOR336W

2.6e-05

-2

iYOL119C

2.9e-05

iYBR249C

2.9e-05

iYOR301W

4.2e-05

iYBR115C

4.6e-05

iYDR034C

5.8e-05

iYJL200C

6.3e-05

-2

iYJR111C

7.6e-05

-2

iYBR248C

0.00012

iYNR050C

0.00013

iYBR144C

0.00014

iYPR110C

0.00016

iYOL154W

0.0002

-2

iYJL072C

0.00021

-2

iYPL274W

0.00023

-2

iYHR070W

0.00025

iYGR271W

0.00028

-2

iYBL076C

0.00028

-2

iYLL005C

0.0005

iYEL062W

0.00053

itT(AGU)J

0.00055

iYDR235W

0.00058

-2

iYJLWdelta9

0.00061

iYDR125C

0.00081

iYDR084C

0.00081

-2

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	875	900	925	950	975

Motif 2 in BLOCKS format

BL   MOTIF 2 width=11 seqs=58
iYEL063C                 (  363) GGGTGAGTCAT  1 
iYER068W                 (  375) GACTGAGTCAT  1 
iYBR113W                 (  487) GGCTGAGTCAC  1 
iYHR161C                 (  407) GGCTGAGTCAC  1 
iYGL184C                 (  386) GGCTGACTCAT  1 
iYOL064C                 (  148) GTCTGAGTCAT  1 
iYDL171C                 (  571) GTCTGAGTCAT  1 
iYOR221C                 (  341) CACTGAGTCAT  1 
iYDR126W                 (    7) GGATGAGTCAT  1 
iYJR109C                 (  345) GGATGAGTCAT  1 
iYJR016C                 (  130) TACTGAGTCAT  1 
iYGR267C                 (   47) GCGTGACTCAT  1 
iYMR062C                 (  148) CAGTGAGTCAT  1 
iYER089C                 (  451) TGCTGACTCAT  1 
iYBR043C                 (  346) GAATGAGTCAT  1 
iYER052C                 (  289) AGGTGAGTCAT  1 
iYNL005C                 (  612) TGGTGAGTCAC  1 
iYLR355C                 (  298) GGATGAGTCAC  1 
iYHR018C                 (  183) AAGTGAGTCAT  1 
iYOR130C                 (  227) AGGTGAGTCAC  1 
iYOR107W                 (  489) GAATGACTCAT  1 
iYOL059W                 (  422) TAGTGACTCAT  1 
iYDR341C                 (  195) AACTGACTCAT  1 
iYNL104C                 (   95) AACTGAGTCAC  1 
iYKL016C                 (  331) GATTGAGTCAT  1 
iYGL126W                 (    1) TCCTGAGTCAT  1 
iYDL198C                 (  137) CAGTGACTCAC  1 
iYCL030C                 (  202) CAGTGACTCAC  1 
iYER055C                 (  192) AAGTGAGTCAC  1 
iYOL141W                 (   43) AAGTGAGTCAC  1 
itM(CAU)P                (  580) CCCTGACTCAT  1 
iYJL089W                 (   82) TCGTGACTCAT  1 
iYER072W                 (  599) TTCTGACTCAT  1 
iYOR336W                 (  206) TAATGAGTCAT  1 
iYOL119C                 (  198) GGCTGACTAAT  1 
iYBR249C                 (  318) CGTTGAGTCAT  1 
iYOR301W                 (  131) GTTTGACTCAT  1 
iYBR115C                 (  165) CATTGAGTCAC  1 
iYDR034C                 (  247) AATTGAGTCAC  1 
iYJL200C                 (  226) TCTTGAGTCAT  1 
iYJR111C                 (  160) GTGTGACTAAT  1 
iYBR248C                 (  112) GTCTGACTCTT  1 
iYNR050C                 (  211) GTATGAGTAAT  1 
iYBR144C                 (  147) TACTGTCTCAC  1 
iYPR110C                 (  245) TTCTGACTAAT  1 
iYOL154W                 (  897) CACTGACTGAC  1 
iYJL072C                 (  138) TGATGACTAAC  1 
iYPL274W                 (  237) AAATGACTAAT  1 
iYHR070W                 (   38) AGATGACTAAC  1 
iYGR271W                 (    1) TTGTGTCTCAC  1 
iYBL076C                 (   87) TGATGACTCTT  1 
iYLL005C                 (  108) ATTTGTGTCAT  1 
iYEL062W                 (  201) AACTGAGTATT  1 
itT(AGU)J                (   84) GTGAGAGTAAT  1 
iYDR235W                 (   92) GCGGGAGTGAT  1 
iYJLWdelta9              (  224) CCGTAACTCAT  1 
iYDR125C                 (  372) GGTAGTGTCAT  1 
iYDR084C                 (  229) GAAGGCGTCAT  1 
//

Motif 2 position-specific scoring matrix

log-odds matrix: alength= 4 w= 11 n= 32709 bayes= 9.77853 E= 1.1e-014 
   -64    -20    115    -41 
    30    -56     72    -76 
   -64     95     80   -122 
  -322  -1250   -237    153 
  -422  -1250    246  -1250 
   151   -337  -1250   -222 
 -1250    121    172  -1250 
 -1250  -1250  -1250    164 
  -105    218   -237  -1250 
   156  -1250  -1250   -264 
 -1250     72  -1250    114

Motif 2 position-specific probability matrix

letter-probability matrix: alength= 4 w= 11 nsites= 58 E= 1.1e-014 
 0.206897  0.155172  0.396552  0.241379 
 0.396552  0.120690  0.293103  0.189655 
 0.206897  0.344828  0.310345  0.137931 
 0.034483  0.000000  0.034483  0.931034 
 0.017241  0.000000  0.982759  0.000000 
 0.913793  0.017241  0.000000  0.068966 
 0.000000  0.413793  0.586207  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.155172  0.810345  0.034483  0.000000 
 0.948276  0.000000  0.000000  0.051724 
 0.000000  0.293103  0.000000  0.706897






Time 315.57 secs.

MOTIF 3 width = 11 sites = 8 llr = 110 E-value = 8.8e+004

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	:	:	6	:	:	:	:	:	3	1
				pos.-specific	C	:	a	:	3	:	8	:	1	a	1	1
				probability	G	a	:	a	:	a	3	9	9	:	4	8
				matrix	T	:	:	:	1	:	:	1	:	:	3	:
.
				bits	2.5
					2.2
					2.0
					1.7
				Information	1.5
				content	1.2
				(19.9 bits)	1.0
					0.7
					0.5
					0.2
					0.0
.
				Multilevel		`G`	`C`	`G`	`A`	`G`	`C`	`G`	`G`	`C`	`G`	`G`
				consensus					`C`		`G`				`A`
				sequence											`T`

.
iYHR161C	-	280	1.04e-08	`ACTCTTGGAA`		`G`	`C`	`G`	`A`	`G`	`C`	`G`	`G`	`C`	`G`	`G`	`GTTCCATCAC`
iYER052C	+	491	5.39e-08	`AGATTCAATC`		`G`	`C`	`G`	`A`	`G`	`C`	`G`	`G`	`C`	`T`	`G`	`GCAAGTTTGG`
iYOR301W	+	69	1.98e-07	`ACAAGAAACA`		`G`	`C`	`G`	`A`	`G`	`G`	`G`	`G`	`C`	`C`	`G`	`TTAAGTGCAG`
iYHR070W	+	67	2.19e-07	`CTTCGAGAAG`		`G`	`C`	`G`	`C`	`G`	`G`	`G`	`G`	`C`	`T`	`G`	`ACAGGGCACT`
itM(CAU)P	-	835	2.44e-07	`GAAAAATTCA`		`G`	`C`	`G`	`A`	`G`	`C`	`G`	`G`	`C`	`G`	`A`	`TGCGCTGTTG`
iYPL274W	-	88	4.17e-07	`GCTTAACAAT`		`G`	`C`	`G`	`A`	`G`	`C`	`G`	`C`	`C`	`A`	`G`	`GCTATAAAAT`
iYOR107W	-	452	4.80e-07	`GACCATGATG`		`G`	`C`	`G`	`C`	`G`	`C`	`G`	`G`	`C`	`A`	`C`	`CAAAATAGAC`
iYBL076C	+	115	1.09e-06	`GAGATTTCTT`		`G`	`C`	`G`	`T`	`G`	`C`	`T`	`G`	`C`	`G`	`G`	`AAACAAAAAA`

Motif 3 block diagrams

Name

Lowest
p-value

Motifs

iYHR161C

1e-08

-3

iYER052C

5.4e-08

iYOR301W

2e-07

iYHR070W

2.2e-07

itM(CAU)P

2.4e-07

-3

iYPL274W

4.2e-07

-3

iYOR107W

4.8e-07

-3

iYBL076C

1.1e-06

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	875	900	925	950	975

Motif 3 in BLOCKS format

BL   MOTIF 3 width=11 seqs=8
iYHR161C                 (  280) GCGAGCGGCGG  1 
iYER052C                 (  491) GCGAGCGGCTG  1 
iYOR301W                 (   69) GCGAGGGGCCG  1 
iYHR070W                 (   67) GCGCGGGGCTG  1 
itM(CAU)P                (  835) GCGAGCGGCGA  1 
iYPL274W                 (   88) GCGAGCGCCAG  1 
iYOR107W                 (  452) GCGCGCGGCAC  1 
iYBL076C                 (  115) GCGTGCTGCGG  1 
//

Motif 3 position-specific scoring matrix

log-odds matrix: alength= 4 w= 11 n= 32709 bayes= 11.997 E= 8.8e+004 
  -965   -965    249   -965 
  -965    249   -965   -965 
  -965   -965    249   -965 
    96     49   -965   -136 
  -965   -965    249   -965 
  -965    207     49   -965 
  -965   -965    229   -136 
  -965    -51    229   -965 
  -965    249   -965   -965 
   -36    -51    107    -36 
  -136    -51    207   -965

Motif 3 position-specific probability matrix

letter-probability matrix: alength= 4 w= 11 nsites= 8 E= 8.8e+004 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.625000  0.250000  0.000000  0.125000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.750000  0.250000  0.000000 
 0.000000  0.000000  0.875000  0.125000 
 0.000000  0.125000  0.875000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.250000  0.125000  0.375000  0.250000 
 0.125000  0.125000  0.750000  0.000000






Time 465.48 secs.

MOTIF 4 width = 11 sites = 11 llr = 138 E-value = 3.0e+006

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	:	:	:	:	:	:	:	:	:	:
				pos.-specific	C	a	7	3	1	8	8	:	a	8	a	6
				probability	G	:	1	2	:	2	:	2	:	2	:	:
				matrix	T	:	2	5	9	:	2	8	:	:	:	4
.
				bits	2.5
					2.2
					2.0
					1.7
				Information	1.5
				content	1.2
				(18.2 bits)	1.0
					0.7
					0.5
					0.2
					0.0
.
				Multilevel		`C`	`C`	`T`	`T`	`C`	`C`	`T`	`C`	`C`	`C`	`C`
				consensus				`C`								`T`
				sequence

.
iYHR161C	+	75	3.40e-08	`CAGGTTTTGT`		`C`	`C`	`T`	`T`	`C`	`C`	`T`	`C`	`C`	`C`	`C`	`CACCAAAAAG`
iYER089C	-	209	5.28e-08	`AAAAAATTCA`		`C`	`C`	`C`	`T`	`C`	`C`	`T`	`C`	`C`	`C`	`C`	`ACGGAATAAA`
iYGL126W	+	296	2.75e-07	`GTGTAGTTTG`		`C`	`C`	`T`	`T`	`G`	`C`	`T`	`C`	`C`	`C`	`C`	`TTGATTGAAA`
iYOL059W	+	18	3.75e-07	`ACACTCTCCC`		`C`	`C`	`C`	`C`	`C`	`C`	`T`	`C`	`C`	`C`	`C`	`CTCTGATCTT`
iYOR336W	+	195	6.56e-07	`CGAGTTTTGC`		`C`	`C`	`G`	`T`	`G`	`C`	`T`	`C`	`C`	`C`	`C`	`ATGACTCATT`
iYNR050C	+	1188	8.10e-07	`GCATTCATTC`		`C`	`C`	`T`	`T`	`C`	`C`	`G`	`C`	`G`	`C`	`C`	`AGTATATTAG`
iYHR018C	-	428	1.57e-06	`TTAATATTTA`		`C`	`G`	`T`	`T`	`C`	`C`	`T`	`C`	`C`	`C`	`T`	`CTCTCTAATT`
iYJR016C	-	248	1.84e-06	`TGTATCCATT`		`C`	`C`	`G`	`T`	`C`	`C`	`T`	`C`	`G`	`C`	`T`	`GAACCCATGA`
iYBR113W	+	831	1.94e-06	`GTAGTACATC`		`C`	`C`	`C`	`T`	`C`	`T`	`T`	`C`	`C`	`C`	`T`	`TTGATTTTTA`
iYJLWdelta9	-	318	3.18e-06	`CCAGTCAATT`		`C`	`T`	`T`	`T`	`C`	`C`	`G`	`C`	`C`	`C`	`T`	`TTGCATCTAT`
iYDL171C	-	172	3.18e-06	`CTCAGTTGCT`		`C`	`T`	`T`	`T`	`C`	`T`	`T`	`C`	`C`	`C`	`C`	`TTCTTTTAGC`

Motif 4 block diagrams

Name

Lowest
p-value

Motifs

iYHR161C

3.4e-08

iYER089C

5.3e-08

-4

iYGL126W

2.7e-07

iYOL059W

3.8e-07

iYOR336W

6.6e-07

iYNR050C

8.1e-07

iYHR018C

1.6e-06

-4

iYJR016C

1.8e-06

-4

iYBR113W

1.9e-06

iYJLWdelta9

3.2e-06

-4

iYDL171C

3.2e-06

-4

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	875	900	925	950	975

Motif 4 in BLOCKS format

BL   MOTIF 4 width=11 seqs=11
iYHR161C                 (   75) CCTTCCTCCCC  1 
iYER089C                 (  209) CCCTCCTCCCC  1 
iYGL126W                 (  296) CCTTGCTCCCC  1 
iYOL059W                 (   18) CCCCCCTCCCC  1 
iYOR336W                 (  195) CCGTGCTCCCC  1 
iYNR050C                 ( 1188) CCTTCCGCGCC  1 
iYHR018C                 (  428) CGTTCCTCCCT  1 
iYJR016C                 (  248) CCGTCCTCGCT  1 
iYBR113W                 (  831) CCCTCTTCCCT  1 
iYJLWdelta9              (  318) CTTTCCGCCCT  1 
iYDL171C                 (  172) CTTTCTTCCCC  1 
//

Motif 4 position-specific scoring matrix

log-odds matrix: alength= 4 w= 11 n= 32709 bayes= 13.0712 E= 3.0e+006 
 -1010    249  -1010  -1010 
 -1010    203    -97    -82 
 -1010     61      3     76 
 -1010    -97  -1010    150 
 -1010    220      3  -1010 
 -1010    220  -1010    -82 
 -1010  -1010      3    135 
 -1010    249  -1010  -1010 
 -1010    220      3  -1010 
 -1010    249  -1010  -1010 
 -1010    183  -1010     18

Motif 4 position-specific probability matrix

letter-probability matrix: alength= 4 w= 11 nsites= 11 E= 3.0e+006 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.727273  0.090909  0.181818 
 0.000000  0.272727  0.181818  0.545455 
 0.000000  0.090909  0.000000  0.909091 
 0.000000  0.818182  0.181818  0.000000 
 0.000000  0.818182  0.000000  0.181818 
 0.000000  0.000000  0.181818  0.818182 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.818182  0.181818  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.636364  0.000000  0.363636






Time 619.53 secs.

MOTIF 5 width = 11 sites = 6 llr = 86 E-value = 5.6e+005

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	3	:	2	:	:	2	:	:	:	:
				pos.-specific	C	2	5	8	:	2	:	:	8	:	:	a
				probability	G	8	2	2	8	8	:	8	2	a	a	:
				matrix	T	:	:	:	:	:	a	:	:	:	:	:
.
				bits	2.5
					2.2
					2.0
					1.7
				Information	1.5
				content	1.2
				(20.6 bits)	1.0
					0.7
					0.5
					0.2
					0.0
.
				Multilevel		`G`	`C`	`C`	`G`	`G`	`T`	`G`	`C`	`G`	`G`	`C`
				consensus			`A`
				sequence

.
itM(CAU)P	-	667	2.93e-08	`GATCGCGGGC`		`G`	`A`	`C`	`G`	`G`	`T`	`G`	`C`	`G`	`G`	`C`	`ATCGAAAAAG`
iYPL274W	+	113	3.97e-08	`TTAAGCAACA`		`G`	`G`	`C`	`G`	`G`	`T`	`G`	`C`	`G`	`G`	`C`	`AACGTTGAAA`
iYOL154W	+	661	1.19e-07	`AAGTTGTAAT`		`G`	`C`	`C`	`A`	`G`	`T`	`G`	`C`	`G`	`G`	`C`	`TGAACAGAAT`
iYOR130C	+	169	1.94e-07	`GGCGATTCTT`		`G`	`A`	`C`	`G`	`C`	`T`	`G`	`C`	`G`	`G`	`C`	`CACAGCGGCC`
iYBR249C	+	361	4.04e-07	`ACAGGGTGCA`		`G`	`C`	`G`	`G`	`G`	`T`	`G`	`G`	`G`	`G`	`C`	`CACGTTTTAA`
iYGR267C	-	296	5.55e-07	`ATTTGGATGA`		`C`	`C`	`C`	`G`	`G`	`T`	`A`	`C`	`G`	`G`	`C`	`CTTAGTAGAA`

Motif 5 block diagrams

Name

Lowest
p-value

Motifs

itM(CAU)P

2.9e-08

-5

iYPL274W

4e-08

iYOL154W

1.2e-07

iYOR130C

1.9e-07

iYBR249C

4e-07

iYGR267C

5.5e-07

-5

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	875	900	925	950	975

Motif 5 in BLOCKS format

BL   MOTIF 5 width=11 seqs=6
itM(CAU)P                (  667) GACGGTGCGGC  1 
iYPL274W                 (  113) GGCGGTGCGGC  1 
iYOL154W                 (  661) GCCAGTGCGGC  1 
iYOR130C                 (  169) GACGCTGCGGC  1 
iYBR249C                 (  361) GCGGGTGGGGC  1 
iYGR267C                 (  296) CCCGGTACGGC  1 
//

Motif 5 position-specific scoring matrix

log-odds matrix: alength= 4 w= 11 n= 32709 bayes= 13.5118 E= 5.6e+005 
  -923    -10    222   -923 
     5    149    -10   -923 
  -923    222    -10   -923 
   -95   -923    222   -923 
  -923    -10    222   -923 
  -923   -923   -923    163 
   -95   -923    222   -923 
  -923    222    -10   -923 
  -923   -923    249   -923 
  -923   -923    249   -923 
  -923    249   -923   -923

Motif 5 position-specific probability matrix

letter-probability matrix: alength= 4 w= 11 nsites= 6 E= 5.6e+005 
 0.000000  0.166667  0.833333  0.000000 
 0.333333  0.500000  0.166667  0.000000 
 0.000000  0.833333  0.166667  0.000000 
 0.166667  0.000000  0.833333  0.000000 
 0.000000  0.166667  0.833333  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.166667  0.000000  0.833333  0.000000 
 0.000000  0.833333  0.166667  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000






Time 770.53 secs.

SUMMARY OF MOTIFS

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

Name

Combined
p-value

Motifs

iYJR109C

2.58e-02

-1

iYDR126W

1.40e-03

-2

iYHR018C

4.28e-05

-1

-4

iYER052C

2.34e-06

-1

-5

iYOL141W

1.63e-03

-3

-2

-1

iYJL089W

1.10e-02

-2

iYOL059W

8.49e-05

-4

iYER055C

1.78e-02

-2

iYMR062C

2.86e-04

-3

iYLR355C

5.27e-03

iYKL016C

1.79e-01

iYEL063C

4.12e-03

-1

-2

-1

iYOR336W

4.67e-05

-2

iYER068W

4.89e-04

-1

-2

iYOR107W

1.34e-04

-3

-1

iYCL030C

3.75e-02

-1

-2

iYHR070W

1.91e-04

-1

iYDL198C

6.81e-03

iYDL171C

1.69e-04

-1

-4

-1

iYNL005C

4.50e-02

-1

iYDR481C

8.01e-02

iYGL184C

4.19e-03

-2

iYOL064C

6.72e-03

iYOR301W

5.69e-06

iYOR130C

2.18e-03

iYBR115C

2.63e-02

iYJL200C

1.22e-02

-2

-1

iYLL005C

1.48e-01

-1

itT(AGU)J

4.57e-01

iYBR043C

1.91e-02

-2

iYDR084C

2.10e-01

iYOL154W

2.38e-03

-4

iYDR235W

7.64e-02

iYBR249C

3.03e-04

-1

iYPR110C

3.51e-01

iYER072W

1.58e-02

-1

iYHR161C

3.31e-10

-3

-4

-1

iYBR113W

2.78e-06

-1

-4

-2

-5

iYJL072C

8.95e-03

-1

iYBL076C

1.70e-04

-1

iYOL119C

4.84e-02

iYJR111C

2.60e-02

-2

-1

iYGR267C

5.65e-06

-2

-5

iYGR271W

4.10e-01

iYJLWdelta9

5.86e-02

-4

iYER089C

9.16e-06

-1

-4

-1

iYNL104C

1.42e-02

-5

iYJR016C

2.26e-07

-1

-3

-4

iYOR221C

1.23e-02

-2

iYPL274W

4.51e-07

-3

-1

iYEL062W

8.12e-02

iYBR248C

5.72e-02

-2

iYDR341C

1.53e-02

iYNR050C

1.63e-03

-5

-1

iYDR125C

5.52e-01

iYBR144C

2.29e-01

itM(CAU)P

1.68e-07

-5

-3

-5

iYDR034C

8.13e-02

iYGL126W

1.17e-05

-2

-1

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	875	900	925	950	975	1000	1025	1050

Stopped because nmotifs = 5 reached.


CPU: ncc007

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 ("a" means 10). 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 PROPERTIES

A, C, F, I, L, V, W and M BLUE Most hydrophobic[Kyte and Doolittle, 1982]

NQST GREEN Polar, non-charged, non-aliphatic residues

DE MAGENTA Acidic

KR RED Positively charged

H PINK

G ORANGE

P YELLOW

Y TURQUOISE

J. Kyte and R. Doolittle, 1982. "A Simple Method for Displaying the Hydropathic Character of a Protein", J. Mol Biol. 157, 105-132.

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.) Each entry in the matrix is multiplied by 100 and rounded to the nearest integer before printing. 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 a scoring threshold.
Position-Specific Probability Matrix
The motif itself is a position-specific probability matrix giving, for each position in the pattern, the observed frequency ("probability") of each possible letter. 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, number of occurrences of the motif, and the E-value of the motif.
Note: Earlier versions of MEME gave the posterior probabilities--the probability after applying a prior on letter frequencies--rather than the observed frequencies. These versions of MEME also gave the number of possible positions for the motif rather than the actual number of occurrences. The output from these earlier versions of MEME can be distinguished by "n=" rather than "nsites=" in the line preceding the matrix.

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AMINO ACIDS	COLOR	PROPERTIES
A, C, F, I, L, V, W and M	BLUE	Most hydrophobic[Kyte and Doolittle, 1982]
NQST	GREEN	Polar, non-charged, non-aliphatic residues
DE	MAGENTA	Acidic
KR	RED	Positively charged
H	PINK
G	ORANGE
P	YELLOW
Y	TURQUOISE

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