Marc Rehmsmeier - PRE analysis

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= hits_30.fasta
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
3R_12589500_12590299_(80 1.0000    800  3R_25386700_25387599_(90 1.0000    900  
3R_21504100_21504899_(80 1.0000    800  2L_5413600_5414399_(800) 1.0000    800  
X_14247600_14248299_(700 1.0000    700  3R_17378100_17378799_(70 1.0000    700  
2L_14472300_14473199_(90 1.0000    900  3L_1107600_1108399_(800) 1.0000    800  
2R_5039100_5039899_(800) 1.0000    800  2L_11434600_11435499_(90 1.0000    900  
X_17098500_17099199_(700 1.0000    700  2R_14030000_14030899_(90 1.0000    900  
X_17508500_17509199_(700 1.0000    700  X_9717100_9717899_(800)  1.0000    800  
X_13798600_13799299_(700 1.0000    700  3R_22366000_22366799_(80 1.0000    800  
X_16943800_16944599_(800 1.0000    800  X_11044500_11045199_(700 1.0000    700  
2R_6957200_6957899_(700) 1.0000    700  2R_14356700_14357399_(70 1.0000    700  
2L_20746400_20747199_(80 1.0000    800  3R_8837700_8838499_(800) 1.0000    800  
X_17980400_17981199_(800 1.0000    800  X_10896100_10896799_(700 1.0000    700  
X_8717700_8718299_(600)  1.0000    600  3L_19484500_19485299_(80 1.0000    800  
2R_8758700_8759399_(700) 1.0000    700  3L_6076100_6076799_(700) 1.0000    700  
X_3050400_3051099_(700)  1.0000    700  3R_14525400_14526099_(70 1.0000    700

COMMAND LINE SUMMARY

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

command: meme hits_30.fasta -dna -mod tcm -minw 6 -maxw 12 -nmotifs 10 -revcomp 

model:  mod=           tcm    nmotifs=        10    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           12    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=       50    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=           22900    N=              30
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.261 C 0.239 G 0.239 T 0.261 
Background letter frequencies (from dataset with add-one prior applied):
A 0.261 C 0.239 G 0.239 T 0.261

P N
MOTIF 1 width = 12 sites = 50 llr = 668 E-value = 8.0e-093

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	8	1	a	1	6	:	9	:	9	:	8	:
				pos.-specific	C	2	:	:	:	3	:	:	:	1	:	1	:
				probability	G	:	9	:	9	:	a	1	a	:	a	2	a
				matrix	T	:	:	:	:	:	:	:	:	:	:	:	:
.
				bits	2.1
					1.9
					1.7
					1.4
				Information	1.2
				content	1.0
				(19.3 bits)	0.8
					0.6
					0.4
					0.2
					0.0
.
				Multilevel		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`
				consensus						`C`
				sequence

.

X_3050400_3051099_(700)	+	310	5.89e-08	`ACAGAGAGCG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`AGAAAGAGAG`
3L_6076100_6076799_(700)	-	417	5.89e-08	`AAAGAGAGAG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`AACGTCGCCT`
X_8717700_8718299_(600)	-	212	5.89e-08	`AGAGAGAGAG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`TGATGGCGTG`
3R_8837700_8838499_(800)	+	399	5.89e-08	`TGAGTGAGTG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`AGAGAGCAAT`
2R_14356700_14357399_(70	-	224	5.89e-08	`CAAGAGAGAG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`CAAAAAACAG`
2R_6957200_6957899_(700)	-	485	5.89e-08	`AGAGGAATAG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`ACCAAAATGG`
X_11044500_11045199_(700	+	343	5.89e-08	`GAGAGAGGTG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`AGAGAGAGGA`
X_13798600_13799299_(700	+	228	5.89e-08	`CGAGAGAGGG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`AGCGCGAGCG`
X_17098500_17099199_(700	-	200	5.89e-08	`AGAGAGAGAG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`ATCTCTATAC`
2R_5039100_5039899_(800)	-	538	5.89e-08	`CCCGAGCTGG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`TTCCGATTTG`
3L_1107600_1108399_(800)	-	463	5.89e-08	`ATCGGGACCG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`ATAGAGGAAT`
3R_17378100_17378799_(70	-	234	5.89e-08	`AGAGAGAGAG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`AAAGTGGGTG`
X_14247600_14248299_(700	-	209	5.89e-08	`ACAGCGAGAC`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`GGAGAGAGTG`
2L_5413600_5414399_(800)	+	503	5.89e-08	`CGCGCAAGAC`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`AGAGAGCGAG`
3R_25386700_25387599_(90	+	389	5.89e-08	`GTGCAGAAAA`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`CGGAAGAGAG`
X_8717700_8718299_(600)	+	481	1.13e-07	`AGAGAGAGCG`		`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`GGTGTGAGAC`
2L_14472300_14473199_(90	+	469	1.13e-07	`GCCAAATCGG`		`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`AGAAAACCTG`
3R_17378100_17378799_(70	+	419	1.13e-07	`AGTCACTCGA`		`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`CGCGTTGTGT`
3R_12589500_12590299_(80	-	82	1.13e-07	`TTTTGTTGCT`		`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`CAGCGTAAAA`
2L_11434600_11435499_(90	-	289	1.67e-07	`CCCGAGAGAA`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`AGTAATGAAG`
3R_25386700_25387599_(90	-	682	1.67e-07	`AGTGTGTGTG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`TTGGAGCTGT`
X_17508500_17509199_(700	-	343	2.75e-07	`CGAGAGTGGG`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`CGAGAGCGGG`
X_17508500_17509199_(700	-	534	3.79e-07	`GGCGAGCGAA`		`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`CGAGCGTGAA`
2L_14472300_14473199_(90	+	295	3.79e-07	`AGAGAGACAC`		`A`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`A`	`G`	`A`	`G`	`TGAGCGTGAC`
3R_25386700_25387599_(90	+	407	3.79e-07	`AGAGCGGAAG`		`A`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`A`	`G`	`A`	`G`	`GACGTGAGTG`
3R_12589500_12590299_(80	+	390	3.79e-07	`GCGACTGCGG`		`A`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`A`	`G`	`A`	`G`	`ATACGGTTAG`
2L_20746400_20747199_(80	-	443	5.32e-07	`GAGCAGATGC`		`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`TGAGCGAGCG`
2L_11434600_11435499_(90	-	407	5.32e-07	`ATTAATCGAG`		`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`ATGGGGCATT`
2L_11434600_11435499_(90	-	106	5.32e-07	`AATTATGATG`		`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`AGGCGCATAT`
2L_14472300_14473199_(90	+	69	5.81e-07	`GTGAAGTGCC`		`A`	`G`	`A`	`G`	`C`	`G`	`G`	`G`	`A`	`G`	`A`	`G`	`CGACAAACAA`
X_3050400_3051099_(700)	+	322	7.59e-07	`AGAGAGAGAG`		`A`	`G`	`A`	`A`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`GGAAAAGACA`
X_8717700_8718299_(600)	+	467	7.59e-07	`TGCGAGCGCG`		`A`	`A`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`CGAGAGCGAG`
X_11044500_11045199_(700	+	328	7.59e-07	`GACATCATCG`		`A`	`G`	`A`	`A`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`GTGAGAGAGA`
2L_11434600_11435499_(90	-	553	7.59e-07	`GAATGGTGAG`		`C`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`AGTGAGTGAG`
X_8717700_8718299_(600)	-	587	8.09e-07	`AG`		`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`A`	`G`	`C`	`G`	`AGCAAGCGAG`
X_17980400_17981199_(800	-	543	9.58e-07	`AAAAGGCGGC`		`C`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`AGACGGCCGT`
2R_14356700_14357399_(70	-	258	1.22e-06	`AGCGTGGGTG`		`C`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`AGGGAGAGAG`
X_17508500_17509199_(700	-	288	1.22e-06	`CGAGAGCGTG`		`C`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`AAATTCATCA`
2L_14472300_14473199_(90	+	47	1.22e-06	`TGAGCGGGTC`		`A`	`G`	`A`	`G`	`G`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`GTGAAGTGCC`
2L_20746400_20747199_(80	-	407	1.38e-06	`GGAGGCGAGG`		`T`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`GCCGATGTGG`
3R_14525400_14526099_(70	-	423	1.58e-06	`TGGACAGCGG`		`A`	`G`	`T`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`GGCAGATAAC`
X_13798600_13799299_(700	+	244	1.58e-06	`AGAGAGAGCG`		`C`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`CAAGCAAGAG`
X_17980400_17981199_(800	-	220	1.69e-06	`CATCAGCCGT`		`C`	`G`	`A`	`G`	`C`	`G`	`G`	`G`	`A`	`G`	`A`	`G`	`ACCGTGGAGC`
3R_8837700_8838499_(800)	+	663	1.69e-06	`TTGGTGCGAC`		`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`A`	`A`	`G`	`AGCGAGCTAG`
2L_11434600_11435499_(90	-	66	1.69e-06	`ATATGAAATG`		`C`	`G`	`A`	`G`	`C`	`G`	`G`	`G`	`A`	`G`	`A`	`G`	`CGTACATGCG`
X_17098500_17099199_(700	+	8	1.81e-06	`TTCGATT`		`A`	`G`	`A`	`A`	`A`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`GGCTGTTATC`
2L_5413600_5414399_(800)	+	474	1.81e-06	`AGGGGGAGCG`		`A`	`A`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`CAGTAGACGC`
3R_12589500_12590299_(80	-	509	1.81e-06	`GATAACTCAA`		`A`	`A`	`A`	`G`	`A`	`G`	`A`	`G`	`A`	`G`	`G`	`G`	`CTATTCCAAG`
X_17980400_17981199_(800	+	389	2.22e-06	`TCTGCGAGTG`		`C`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`A`	`G`	`C`	`G`	`CCCGAGTGAG`
2L_5413600_5414399_(800)	+	517	2.81e-06	`AGAGAGAGAG`		`A`	`G`	`A`	`G`	`C`	`G`	`A`	`G`	`C`	`G`	`C`	`G`	`GTTGATGGGT`

Motif 1 block diagrams

Name

Lowest
p-value

Motifs

X_3050400_3051099_(700)

7.6e-07

3L_6076100_6076799_(700)

5.9e-08

-1

X_8717700_8718299_(600)

8.1e-07

-1

3R_8837700_8838499_(800)

1.7e-06

2R_14356700_14357399_(70

1.2e-06

-1

2R_6957200_6957899_(700)

5.9e-08

-1

X_11044500_11045199_(700

7.6e-07

X_13798600_13799299_(700

1.6e-06

X_17098500_17099199_(700

1.8e-06

-1

2R_5039100_5039899_(800)

5.9e-08

-1

3L_1107600_1108399_(800)

5.9e-08

-1

3R_17378100_17378799_(70

1.1e-07

-1

X_14247600_14248299_(700

5.9e-08

-1

2L_5413600_5414399_(800)

2.8e-06

3R_25386700_25387599_(90

3.8e-07

-1

2L_14472300_14473199_(90

1.2e-06

3R_12589500_12590299_(80

1.8e-06

-1

2L_11434600_11435499_(90

1.7e-06

-1

X_17508500_17509199_(700

1.2e-06

-1

2L_20746400_20747199_(80

1.4e-06

-1

X_17980400_17981199_(800

1.7e-06

-1

3R_14525400_14526099_(70

1.6e-06

-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

Motif 1 in BLOCKS format

BL   MOTIF 1 width=12 seqs=50
X_3050400_3051099_(700)  (  310) AGAGAGAGAGAG  1 
3L_6076100_6076799_(700) (  417) AGAGAGAGAGAG  1 
X_8717700_8718299_(600)  (  212) AGAGAGAGAGAG  1 
3R_8837700_8838499_(800) (  399) AGAGAGAGAGAG  1 
2R_14356700_14357399_(70 (  224) AGAGAGAGAGAG  1 
2R_6957200_6957899_(700) (  485) AGAGAGAGAGAG  1 
X_11044500_11045199_(700 (  343) AGAGAGAGAGAG  1 
X_13798600_13799299_(700 (  228) AGAGAGAGAGAG  1 
X_17098500_17099199_(700 (  200) AGAGAGAGAGAG  1 
2R_5039100_5039899_(800) (  538) AGAGAGAGAGAG  1 
3L_1107600_1108399_(800) (  463) AGAGAGAGAGAG  1 
3R_17378100_17378799_(70 (  234) AGAGAGAGAGAG  1 
X_14247600_14248299_(700 (  209) AGAGAGAGAGAG  1 
2L_5413600_5414399_(800) (  503) AGAGAGAGAGAG  1 
3R_25386700_25387599_(90 (  389) AGAGAGAGAGAG  1 
X_8717700_8718299_(600)  (  481) AGAGCGAGAGAG  1 
2L_14472300_14473199_(90 (  469) AGAGCGAGAGAG  1 
3R_17378100_17378799_(70 (  419) AGAGCGAGAGAG  1 
3R_12589500_12590299_(80 (   82) AGAGCGAGAGAG  1 
2L_11434600_11435499_(90 (  289) AGAGAGAGAGGG  1 
3R_25386700_25387599_(90 (  682) AGAGAGAGAGGG  1 
X_17508500_17509199_(700 (  343) AGAGAGAGCGAG  1 
X_17508500_17509199_(700 (  534) AGAGCGAGAGGG  1 
2L_14472300_14473199_(90 (  295) AGAGAGGGAGAG  1 
3R_25386700_25387599_(90 (  407) AGAGAGGGAGAG  1 
3R_12589500_12590299_(80 (  390) AGAGAGGGAGAG  1 
2L_20746400_20747199_(80 (  443) AGAGCGAGCGAG  1 
2L_11434600_11435499_(90 (  407) AGAGCGAGCGAG  1 
2L_11434600_11435499_(90 (  106) AGAGCGAGCGAG  1 
2L_14472300_14473199_(90 (   69) AGAGCGGGAGAG  1 
X_3050400_3051099_(700)  (  322) AGAAAGAGAGAG  1 
X_8717700_8718299_(600)  (  467) AAAGAGAGAGAG  1 
X_11044500_11045199_(700 (  328) AGAAAGAGAGAG  1 
2L_11434600_11435499_(90 (  553) CGAGAGAGAGGG  1 
X_8717700_8718299_(600)  (  587) AGAGCGAGAGCG  1 
X_17980400_17981199_(800 (  543) CGAGAGAGCGAG  1 
2R_14356700_14357399_(70 (  258) CGAGCGAGAGGG  1 
X_17508500_17509199_(700 (  288) CGAGCGAGAGGG  1 
2L_14472300_14473199_(90 (   47) AGAGGGAGAGAG  1 
2L_20746400_20747199_(80 (  407) TGAGAGAGAGAG  1 
3R_14525400_14526099_(70 (  423) AGTGAGAGAGAG  1 
X_13798600_13799299_(700 (  244) CGAGCGAGCGAG  1 
X_17980400_17981199_(800 (  220) CGAGCGGGAGAG  1 
3R_8837700_8838499_(800) (  663) AGAGAGAGAAAG  1 
2L_11434600_11435499_(90 (   66) CGAGCGGGAGAG  1 
X_17098500_17099199_(700 (    8) AGAAAGAGAGGG  1 
2L_5413600_5414399_(800) (  474) AAAGAGAGAGGG  1 
3R_12589500_12590299_(80 (  509) AAAGAGAGAGGG  1 
X_17980400_17981199_(800 (  389) CGAGCGAGAGCG  1 
2L_5413600_5414399_(800) (  517) AGAGCGAGCGCG  1 
//

Motif 1 position-specific scoring matrix

log-odds matrix: alength= 4 w= 12 n= 22570 bayes= 10.4254 E= 8.0e-093 
   165    -58  -1229   -370 
  -212  -1229    197  -1229 
   191  -1229  -1229   -370 
  -212  -1229    197  -1229 
   129     51   -358  -1229 
 -1229  -1229    206  -1229 
   175  -1229    -99  -1229 
 -1229  -1229    206  -1229 
   172    -77  -1229  -1229 
  -370  -1229    203  -1229 
   154   -199    -41  -1229 
 -1229  -1229    206  -1229

Motif 1 position-specific probability matrix

letter-probability matrix: alength= 4 w= 12 n= 22570 E= 8.0e-093 
 0.819888  0.160016  0.000048  0.020048 
 0.060040  0.000048  0.939860  0.000052 
 0.979856  0.000048  0.000048  0.020048 
 0.060040  0.000048  0.939860  0.000052 
 0.639924  0.339980  0.020044  0.000052 
 0.000052  0.000048  0.999848  0.000052 
 0.879876  0.000048  0.120024  0.000052 
 0.000052  0.000048  0.999848  0.000052 
 0.859880  0.140020  0.000048  0.000052 
 0.020048  0.000048  0.979852  0.000052 
 0.759900  0.060036  0.180012  0.000052 
 0.000052  0.000048  0.999848  0.000052






Time 604.26 secs.

P N
MOTIF 2 width = 12 sites = 50 llr = 538 E-value = 4.5e-036

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	:	:	2	:	:	:	a	:	2	1	:
				pos.-specific	C	3	3	8	4	:	a	a	:	:	1	:	5
				probability	G	4	6	:	1	a	:	:	:	:	:	1	:
				matrix	T	3	1	2	3	:	:	:	:	a	8	8	5
.
				bits	2.1
					1.9
					1.7
					1.4
				Information	1.2
				content	1.0
				(15.5 bits)	0.8
					0.6
					0.4
					0.2
					0.0
.
				Multilevel		`G`	`G`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`
				consensus		`C`	`C`	`T`	`T`								`C`
				sequence		`T`			`A`

.

2L_20746400_20747199_(80	+	379	5.40e-08	`TCCCTTCGAT`		`G`	`G`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`TTCCAGCCAC`
X_14247600_14248299_(700	+	267	5.40e-08	`TTTCTGCCTC`		`G`	`G`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`TGTGGGCAAC`
X_14247600_14248299_(700	+	289	1.63e-07	`TGTGGGCAAC`		`G`	`G`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`GTGTTTGCTG`
3R_25386700_25387599_(90	+	581	2.71e-07	`GCGGCTGAGG`		`C`	`G`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`TGCAATTTTC`
3R_14525400_14526099_(70	+	256	3.79e-07	`CAACACTTTC`		`G`	`G`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`GATGGGCGCT`
2R_8758700_8759399_(700)	+	343	3.79e-07	`AGACTCTTGT`		`G`	`G`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`GTCGCTGGCG`
2R_6957200_6957899_(700)	-	332	3.79e-07	`GTAGTGCAGC`		`G`	`G`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`ACCAAAACCA`
3R_21504100_21504899_(80	+	381	3.79e-07	`ACAAAATGAT`		`G`	`G`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`GCATTAAGCC`
X_9717100_9717899_(800)	-	441	1.23e-06	`CCCGCTTTTT`		`C`	`C`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`CCCAGCCATT`
3R_22366000_22366799_(80	-	267	1.40e-06	`GCCACTTCTG`		`T`	`G`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`AGCTATTTTA`
2R_6957200_6957899_(700)	-	167	1.62e-06	`CACGCCACTG`		`G`	`G`	`T`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`AGAATTCCAT`
2L_5413600_5414399_(800)	+	263	1.62e-06	`AAAACTTGCT`		`G`	`G`	`C`	`G`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`GGCGGGGGGG`
3L_19484500_19485299_(80	+	485	1.84e-06	`CCTATGCAGC`		`T`	`C`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`AACTTATGCG`
X_10896100_10896799_(700	-	193	2.14e-06	`GATTGCAAGC`		`G`	`G`	`T`	`T`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`ACTCCAACGC`
X_9717100_9717899_(800)	-	429	2.14e-06	`CCGCCATTTT`		`C`	`C`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`CCCAGACCCC`
3L_19484500_19485299_(80	+	632	2.47e-06	`CCTATGCTGC`		`T`	`C`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`AACATACTCA`
3L_19484500_19485299_(80	+	314	2.47e-06	`ACTCCACTGG`		`T`	`C`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`GAAGGTAGCA`
3L_19484500_19485299_(80	+	287	2.47e-06	`CGTATGCAGC`		`T`	`C`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`AAGCTACTCC`
2R_8758700_8759399_(700)	+	418	3.10e-06	`GCGGCATCGT`		`T`	`G`	`T`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`TGTTTATGGC`
3R_21504100_21504899_(80	-	355	3.10e-06	`TTTTGTTTTT`		`T`	`C`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`CTTTCCGTTT`
X_16943800_16944599_(800	-	417	3.82e-06	`CCAGTGTAAC`		`C`	`G`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`A`	`T`	`C`	`CTCCACCATA`
X_16943800_16944599_(800	-	252	3.82e-06	`GAACCATAGC`		`C`	`G`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`A`	`T`	`C`	`CAGATCCATA`
3R_22366000_22366799_(80	-	528	3.82e-06	`TGCCATGGCA`		`C`	`G`	`T`	`T`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`GCTTATTGCA`
3R_22366000_22366799_(80	-	395	3.82e-06	`GCAATTTTAT`		`G`	`G`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`T`	`G`	`T`	`TGAGAGCAAA`
2R_8758700_8759399_(700)	+	272	4.62e-06	`CGTGAAAGGT`		`C`	`G`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`G`	`C`	`CATCGCCATC`
X_9717100_9717899_(800)	-	315	5.74e-06	`TGCACGTTTG`		`C`	`C`	`T`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`AGGCGACTGC`
3R_8837700_8838499_(800)	+	421	6.35e-06	`AGAGAGCAAT`		`G`	`C`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`A`	`T`	`T`	`CTATGCAAAA`
3L_19484500_19485299_(80	+	434	6.98e-06	`CCAAGCCTGC`		`G`	`G`	`T`	`G`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`AGCCGCTCCA`
X_8717700_8718299_(600)	+	373	6.98e-06	`TCTCCGCAGT`		`T`	`C`	`T`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`TCCGCTCTAC`
X_16943800_16944599_(800	+	481	6.98e-06	`TGGGCGCTGC`		`G`	`C`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`A`	`T`	`C`	`CACCTCCGCC`
X_9717100_9717899_(800)	+	109	6.98e-06	`TTGGTTCGAT`		`T`	`G`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`T`	`G`	`T`	`TTTTCTTTTG`
3L_1107600_1108399_(800)	+	439	6.98e-06	`CTCCATTATG`		`G`	`C`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`A`	`T`	`C`	`CTATTCCTCT`
2L_14472300_14473199_(90	+	429	6.98e-06	`GTTGCCGTGG`		`T`	`G`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`A`	`T`	`T`	`ATTATGATTT`
3L_1107600_1108399_(800)	+	264	7.53e-06	`GTCGCCGCTT`		`T`	`G`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`A`	`T`	`C`	`GATGACGCGC`
3R_17378100_17378799_(70	-	390	8.33e-06	`ACTTCCGTTT`		`G`	`G`	`C`	`G`	`G`	`C`	`C`	`A`	`T`	`A`	`T`	`T`	`GAATAGATTT`
3L_6076100_6076799_(700)	+	222	9.21e-06	`AAGCTTTTGA`		`C`	`G`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`A`	`T`	`GGTGGCTCCA`
3R_14525400_14526099_(70	+	551	9.93e-06	`TTTATGCATT`		`C`	`T`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`CTCCTAATCT`
X_17098500_17099199_(700	-	428	1.34e-05	`CATAGGCCAT`		`C`	`G`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`C`	`T`	`C`	`AGCCATCTGA`
X_14247600_14248299_(700	+	171	1.34e-05	`AACCCGTTTC`		`T`	`T`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`CTACCCCCCT`
3R_12589500_12590299_(80	+	443	1.34e-05	`CGCTTTACGG`		`C`	`G`	`C`	`A`	`G`	`C`	`C`	`A`	`T`	`T`	`A`	`T`	`GGTGCGCGTA`
3L_19484500_19485299_(80	+	158	1.44e-05	`ACTCATCTGG`		`G`	`C`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`C`	`T`	`C`	`GAAGCTCTCC`
X_17508500_17509199_(700	-	48	1.44e-05	`GAAGGCGCTG`		`C`	`G`	`T`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`G`	`C`	`CAAAAACGAC`
2L_11434600_11435499_(90	+	481	1.44e-05	`GCCCTTGGCA`		`G`	`C`	`C`	`T`	`G`	`C`	`C`	`A`	`T`	`C`	`T`	`C`	`ACTTGCTCTA`
2R_14030000_14030899_(90	+	263	1.54e-05	`TCGGCTGAGA`		`G`	`G`	`G`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`AGCGCTTCAT`
3L_6076100_6076799_(700)	+	249	1.66e-05	`CTCCACCCAC`		`C`	`G`	`T`	`T`	`G`	`C`	`C`	`A`	`T`	`T`	`G`	`T`	`CCCCAGTGTG`
3L_19484500_19485299_(80	-	36	1.66e-05	`CTCCGTAGCT`		`G`	`G`	`C`	`C`	`G`	`C`	`C`	`A`	`C`	`T`	`T`	`T`	`GGTGATCGCC`
2R_5039100_5039899_(800)	+	126	1.77e-05	`TGCGGGCAGG`		`G`	`G`	`C`	`G`	`G`	`C`	`C`	`A`	`T`	`T`	`A`	`T`	`CTCGCTACAG`
X_9717100_9717899_(800)	-	465	2.18e-05	`CTGAGCCGCC`		`C`	`C`	`T`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`G`	`T`	`TCCCCGCTTT`
2R_6957200_6957899_(700)	+	294	2.52e-05	`GCATCAGCTA`		`T`	`T`	`T`	`C`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`CAACCGACTC`
2R_14356700_14357399_(70	-	451	3.37e-05	`ATTTCGAAAA`		`G`	`A`	`C`	`G`	`G`	`C`	`C`	`A`	`T`	`T`	`T`	`C`	`GAGGGAGTTT`

Motif 2 block diagrams

Name

Lowest
p-value

Motifs

2L_20746400_20747199_(80

5.4e-08

X_14247600_14248299_(700

1.3e-05

3R_25386700_25387599_(90

2.7e-07

3R_14525400_14526099_(70

9.9e-06

2R_8758700_8759399_(700)

3.1e-06

2R_6957200_6957899_(700)

2.5e-05

-2

3R_21504100_21504899_(80

3.1e-06

-2

X_9717100_9717899_(800)

2.2e-05

-2

3R_22366000_22366799_(80

3.8e-06

-2

2L_5413600_5414399_(800)

1.6e-06

3L_19484500_19485299_(80

1.7e-05

-2

X_10896100_10896799_(700

2.1e-06

-2

X_16943800_16944599_(800

7e-06

-2

3R_8837700_8838499_(800)

6.3e-06

X_8717700_8718299_(600)

7e-06

3L_1107600_1108399_(800)

7e-06

2L_14472300_14473199_(90

7e-06

3R_17378100_17378799_(70

8.3e-06

-2

3L_6076100_6076799_(700)

1.7e-05

X_17098500_17099199_(700

1.3e-05

-2

3R_12589500_12590299_(80

1.3e-05

X_17508500_17509199_(700

1.4e-05

-2

2L_11434600_11435499_(90

1.4e-05

2R_14030000_14030899_(90

1.5e-05

2R_5039100_5039899_(800)

1.8e-05

2R_14356700_14357399_(70

3.4e-05

-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

Motif 2 in BLOCKS format

BL   MOTIF 2 width=12 seqs=50
2L_20746400_20747199_(80 (  379) GGCCGCCATTTT  1 
X_14247600_14248299_(700 (  267) GGCCGCCATTTT  1 
X_14247600_14248299_(700 (  289) GGCTGCCATTTT  1 
3R_25386700_25387599_(90 (  581) CGCCGCCATTTT  1 
3R_14525400_14526099_(70 (  256) GGCAGCCATTTT  1 
2R_8758700_8759399_(700) (  343) GGCAGCCATTTT  1 
2R_6957200_6957899_(700) (  332) GGCAGCCATTTT  1 
3R_21504100_21504899_(80 (  381) GGCAGCCATTTT  1 
X_9717100_9717899_(800)  (  441) CCCCGCCATTTT  1 
3R_22366000_22366799_(80 (  267) TGCAGCCATTTC  1 
2R_6957200_6957899_(700) (  167) GGTCGCCATTTT  1 
2L_5413600_5414399_(800) (  263) GGCGGCCATTTT  1 
3L_19484500_19485299_(80 (  485) TCCCGCCATTTC  1 
X_10896100_10896799_(700 (  193) GGTTGCCATTTT  1 
X_9717100_9717899_(800)  (  429) CCCAGCCATTTT  1 
3L_19484500_19485299_(80 (  632) TCCTGCCATTTC  1 
3L_19484500_19485299_(80 (  314) TCCTGCCATTTC  1 
3L_19484500_19485299_(80 (  287) TCCTGCCATTTC  1 
2R_8758700_8759399_(700) (  418) TGTCGCCATTTT  1 
3R_21504100_21504899_(80 (  355) TCCAGCCATTTC  1 
X_16943800_16944599_(800 (  417) CGCCGCCATATC  1 
X_16943800_16944599_(800 (  252) CGCCGCCATATC  1 
3R_22366000_22366799_(80 (  528) CGTTGCCATTTC  1 
3R_22366000_22366799_(80 (  395) GGCTGCCATTGT  1 
2R_8758700_8759399_(700) (  272) CGCCGCCATTGC  1 
X_9717100_9717899_(800)  (  315) CCTCGCCATTTC  1 
3R_8837700_8838499_(800) (  421) GCCTGCCATATT  1 
3L_19484500_19485299_(80 (  434) GGTGGCCATTTC  1 
X_8717700_8718299_(600)  (  373) TCTCGCCATTTC  1 
X_16943800_16944599_(800 (  481) GCCTGCCATATC  1 
X_9717100_9717899_(800)  (  109) TGCTGCCATTGT  1 
3L_1107600_1108399_(800) (  439) GCCTGCCATATC  1 
2L_14472300_14473199_(90 (  429) TGCAGCCATATT  1 
3L_1107600_1108399_(800) (  264) TGCAGCCATATC  1 
3R_17378100_17378799_(70 (  390) GGCGGCCATATT  1 
3L_6076100_6076799_(700) (  222) CGCCGCCATTAT  1 
3R_14525400_14526099_(70 (  551) CTCTGCCATTTT  1 
X_17098500_17099199_(700 (  428) CGCAGCCATCTC  1 
X_14247600_14248299_(700 (  171) TTCAGCCATTTT  1 
3R_12589500_12590299_(80 (  443) CGCAGCCATTAT  1 
3L_19484500_19485299_(80 (  158) GCCTGCCATCTC  1 
X_17508500_17509199_(700 (   48) CGTCGCCATTGC  1 
2L_11434600_11435499_(90 (  481) GCCTGCCATCTC  1 
2R_14030000_14030899_(90 (  263) GGGCGCCATTTC  1 
3L_6076100_6076799_(700) (  249) CGTTGCCATTGT  1 
3L_19484500_19485299_(80 (   36) GGCCGCCACTTT  1 
2R_5039100_5039899_(800) (  126) GGCGGCCATTAT  1 
X_9717100_9717899_(800)  (  465) CCTCGCCATTGT  1 
2R_6957200_6957899_(700) (  294) TTTCGCCATTTC  1 
2R_14356700_14357399_(70 (  451) GACGGCCATTTC  1 
//

Motif 2 position-specific scoring matrix

log-odds matrix: alength= 4 w= 12 n= 22570 bayes= 10.4254 E= 4.5e-036 
 -1229     33     88      0 
  -370     33    137   -212 
 -1229    167   -358    -25 
   -12     59   -126     20 
 -1229  -1229    206  -1229 
 -1229    206  -1229  -1229 
 -1229    206  -1229  -1229 
   194  -1229  -1229  -1229 
 -1229   -358  -1229    191 
   -70   -199  -1229    158 
  -212  -1229    -99    165 
 -1229     94  -1229    105

Motif 2 position-specific probability matrix

letter-probability matrix: alength= 4 w= 12 n= 22570 E= 4.5e-036 
 0.000052  0.299988  0.439960  0.260000 
 0.020048  0.299988  0.619924  0.060040 
 0.000052  0.759896  0.020044  0.220008 
 0.240004  0.359976  0.100028  0.299992 
 0.000052  0.000048  0.999848  0.000052 
 0.000052  0.999848  0.000048  0.000052 
 0.000052  0.999848  0.000048  0.000052 
 0.999852  0.000048  0.000048  0.000052 
 0.000052  0.020044  0.000048  0.979856 
 0.160020  0.060036  0.000048  0.779896 
 0.060040  0.000048  0.120024  0.819888 
 0.000052  0.459956  0.000048  0.539944






Time 1196.89 secs.

P N
MOTIF 3 width = 12 sites = 35 llr = 406 E-value = 1.2e-026

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	2	1	:	1	3	:	:	:	4	1	:
				pos.-specific	C	:	:	:	:	:	2	:	1	:	1	:	3
				probability	G	a	:	9	:	9	:	a	:	a	1	9	:
				matrix	T	:	8	:	a	:	5	:	9	:	4	:	6
.
				bits	2.1
					1.9
					1.7
					1.4
				Information	1.2
				content	1.0
				(16.7 bits)	0.8
					0.6
					0.4
					0.2
					0.0
.
				Multilevel		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`
				consensus			`A`				`A`				`A`		`C`
				sequence

.

3R_14525400_14526099_(70	-	325	5.89e-08	`GTGAGTGTGT`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`GACTGTATGT`
X_13798600_13799299_(700	-	89	5.89e-08	`TACTGCTTGT`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`TTGGCCTTTT`
3R_25386700_25387599_(90	-	124	5.89e-08	`GTGTGTGTAT`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`ATTTACCCTT`
3R_8837700_8838499_(800)	+	209	1.18e-07	`GTGTGCGTGC`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`A`	`G`	`T`	`GTGCGATAAA`
3R_21504100_21504899_(80	+	419	1.18e-07	`TTTGCTGTAC`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`A`	`G`	`T`	`GGTGGTGAGA`
3R_25386700_25387599_(90	-	276	1.18e-07	`GTGCTTCTGC`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`A`	`G`	`T`	`GTGGTTGAGT`
3R_8837700_8838499_(800)	+	386	3.44e-07	`GTGAGTGCGT`		`G`	`T`	`G`	`T`	`G`	`A`	`G`	`T`	`G`	`A`	`G`	`T`	`GAGAGAGAGA`
3R_8837700_8838499_(800)	+	311	4.52e-07	`GGTGATGCGG`		`G`	`T`	`G`	`T`	`G`	`C`	`G`	`T`	`G`	`T`	`G`	`T`	`GGGTACGCAC`
2R_6957200_6957899_(700)	-	450	4.52e-07	`ATGTGCATTA`		`G`	`T`	`G`	`T`	`G`	`C`	`G`	`T`	`G`	`T`	`G`	`T`	`GACTTGTACA`
3R_21504100_21504899_(80	+	443	4.52e-07	`TGGTGAGAGG`		`G`	`T`	`G`	`T`	`G`	`A`	`G`	`T`	`G`	`T`	`G`	`C`	`TTGTGTGTGT`
2L_11434600_11435499_(90	-	43	5.60e-07	`GTACATGCGT`		`G`	`T`	`G`	`T`	`G`	`A`	`G`	`T`	`G`	`A`	`G`	`C`	`ACAAGGTGGG`
3R_21504100_21504899_(80	+	457	7.32e-07	`GAGTGTGCTT`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`G`	`G`	`T`	`GAGTGGGGCT`
3R_8837700_8838499_(800)	-	472	7.81e-07	`ATCTGTGGCT`		`G`	`T`	`G`	`T`	`G`	`C`	`G`	`T`	`G`	`T`	`G`	`C`	`GGGGAAATTA`
3R_8837700_8838499_(800)	-	327	8.85e-07	`ACTTGGTCAT`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`C`	`G`	`T`	`ACCCACACAC`
3R_14525400_14526099_(70	-	337	9.98e-07	`GTTTTGCCAT`		`G`	`A`	`G`	`T`	`G`	`A`	`G`	`T`	`G`	`T`	`G`	`T`	`GTGTGTGTGT`
X_17980400_17981199_(800	+	420	1.21e-06	`GCGAACGAGC`		`G`	`A`	`G`	`T`	`G`	`A`	`G`	`T`	`G`	`A`	`G`	`T`	`GAGTGAGTGC`
2L_5413600_5414399_(800)	+	663	1.43e-06	`GAGTGCCACG`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`C`	`G`	`A`	`G`	`T`	`GTGTGGCTAC`
2L_11434600_11435499_(90	-	538	1.74e-06	`GAGAGGGAGT`		`G`	`A`	`G`	`T`	`G`	`A`	`G`	`T`	`G`	`A`	`G`	`C`	`GAAAGAGGGC`
3R_14525400_14526099_(70	-	309	2.28e-06	`GTGTGTGACT`		`G`	`T`	`A`	`T`	`G`	`T`	`G`	`T`	`G`	`A`	`G`	`T`	`GTCACGACGA`
3R_25386700_25387599_(90	-	71	2.43e-06	`CAGTGCATCC`		`G`	`T`	`G`	`T`	`G`	`C`	`G`	`T`	`G`	`G`	`G`	`C`	`ATAAATCTCC`
3R_25386700_25387599_(90	-	136	2.76e-06	`GTTTGCTTCT`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`A`	`T`	`GTGTGTGTGT`
2L_11434600_11435499_(90	+	759	3.39e-06	`TGGTGCTCCC`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`A`	`ATATTATGAA`
3L_1107600_1108399_(800)	+	35	4.16e-06	`GTTTCTTCGA`		`G`	`T`	`G`	`T`	`A`	`A`	`G`	`T`	`G`	`T`	`G`	`T`	`ATCTGGATTG`
2R_14030000_14030899_(90	+	552	4.67e-06	`GCATATCGAT`		`G`	`T`	`G`	`T`	`G`	`T`	`G`	`C`	`G`	`C`	`G`	`T`	`AATGGCATAG`
3R_25386700_25387599_(90	+	424	5.66e-06	`GAGAGGACGT`		`G`	`A`	`G`	`T`	`G`	`T`	`G`	`C`	`G`	`A`	`G`	`C`	`GAGAAGGGTC`
3L_6076100_6076799_(700)	-	532	5.89e-06	`CGTTTCGGTA`		`G`	`T`	`A`	`T`	`G`	`T`	`G`	`T`	`G`	`G`	`G`	`T`	`TTTTCTCAGT`
3R_14525400_14526099_(70	-	230	6.76e-06	`GTGTTGAAGT`		`G`	`T`	`G`	`T`	`A`	`A`	`G`	`T`	`G`	`A`	`G`	`C`	`CAAAAAAGAA`
2R_14356700_14357399_(70	+	360	7.49e-06	`ATTGGTGTTC`		`G`	`T`	`G`	`T`	`G`	`T`	`C`	`T`	`G`	`T`	`G`	`C`	`AAGACTGCAC`
2R_5039100_5039899_(800)	-	344	7.49e-06	`TGCCGGCAGA`		`G`	`A`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`A`	`T`	`CCCACTATAT`
X_17508500_17509199_(700	-	1	8.37e-06	`TTTTCTTCAA`		`C`	`T`	`G`	`T`	`G`	`T`	`G`	`T`	`G`	`A`	`G`	`C`
2L_5413600_5414399_(800)	-	451	8.37e-06	`GCTCCCCCTT`		`G`	`A`	`G`	`T`	`G`	`C`	`G`	`T`	`G`	`C`	`G`	`C`	`CGTAGTTCGA`
3R_25386700_25387599_(90	-	697	8.37e-06	`ACGATTGGGA`		`G`	`A`	`A`	`T`	`G`	`A`	`G`	`T`	`G`	`T`	`G`	`T`	`GTGAGAGAGA`
3R_17378100_17378799_(70	-	4	8.76e-06	`CTGCATTTGG`		`G`	`T`	`G`	`T`	`G`	`C`	`G`	`G`	`G`	`T`	`G`	`T`	`ATG`
2L_14472300_14473199_(90	+	30	1.05e-05	`AACAACAGCT`		`G`	`T`	`G`	`C`	`G`	`A`	`G`	`T`	`G`	`A`	`G`	`C`	`GGGTCAGAGG`
2L_11434600_11435499_(90	-	161	1.71e-05	`AAGCACCAGG`		`G`	`A`	`G`	`T`	`G`	`A`	`G`	`C`	`G`	`G`	`G`	`C`	`CGGCAAGAGT`

Motif 3 block diagrams

Name

Lowest
p-value

Motifs

3R_14525400_14526099_(70

6.8e-06

-3

X_13798600_13799299_(700

5.9e-08

-3

3R_25386700_25387599_(90

8.4e-06

-3

3R_8837700_8838499_(800)

7.8e-07

-3

3R_21504100_21504899_(80

4.5e-07

2R_6957200_6957899_(700)

4.5e-07

-3

2L_11434600_11435499_(90

1.7e-05

-3

X_17980400_17981199_(800

1.2e-06

2L_5413600_5414399_(800)

8.4e-06

-3

3L_1107600_1108399_(800)

4.2e-06

2R_14030000_14030899_(90

4.7e-06

3L_6076100_6076799_(700)

5.9e-06

-3

2R_14356700_14357399_(70

7.5e-06

2R_5039100_5039899_(800)

7.5e-06

-3

X_17508500_17509199_(700

8.4e-06

-3

3R_17378100_17378799_(70

8.8e-06

-3

2L_14472300_14473199_(90

1.1e-05

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

Motif 3 in BLOCKS format

BL   MOTIF 3 width=12 seqs=35
3R_14525400_14526099_(70 (  325) GTGTGTGTGTGT  1 
X_13798600_13799299_(700 (   89) GTGTGTGTGTGT  1 
3R_25386700_25387599_(90 (  124) GTGTGTGTGTGT  1 
3R_8837700_8838499_(800) (  209) GTGTGTGTGAGT  1 
3R_21504100_21504899_(80 (  419) GTGTGTGTGAGT  1 
3R_25386700_25387599_(90 (  276) GTGTGTGTGAGT  1 
3R_8837700_8838499_(800) (  386) GTGTGAGTGAGT  1 
3R_8837700_8838499_(800) (  311) GTGTGCGTGTGT  1 
2R_6957200_6957899_(700) (  450) GTGTGCGTGTGT  1 
3R_21504100_21504899_(80 (  443) GTGTGAGTGTGC  1 
2L_11434600_11435499_(90 (   43) GTGTGAGTGAGC  1 
3R_21504100_21504899_(80 (  457) GTGTGTGTGGGT  1 
3R_8837700_8838499_(800) (  472) GTGTGCGTGTGC  1 
3R_8837700_8838499_(800) (  327) GTGTGTGTGCGT  1 
3R_14525400_14526099_(70 (  337) GAGTGAGTGTGT  1 
X_17980400_17981199_(800 (  420) GAGTGAGTGAGT  1 
2L_5413600_5414399_(800) (  663) GTGTGTGCGAGT  1 
2L_11434600_11435499_(90 (  538) GAGTGAGTGAGC  1 
3R_14525400_14526099_(70 (  309) GTATGTGTGAGT  1 
3R_25386700_25387599_(90 (   71) GTGTGCGTGGGC  1 
3R_25386700_25387599_(90 (  136) GTGTGTGTGTAT  1 
2L_11434600_11435499_(90 (  759) GTGTGTGTGTGA  1 
3L_1107600_1108399_(800) (   35) GTGTAAGTGTGT  1 
2R_14030000_14030899_(90 (  552) GTGTGTGCGCGT  1 
3R_25386700_25387599_(90 (  424) GAGTGTGCGAGC  1 
3L_6076100_6076799_(700) (  532) GTATGTGTGGGT  1 
3R_14525400_14526099_(70 (  230) GTGTAAGTGAGC  1 
2R_14356700_14357399_(70 (  360) GTGTGTCTGTGC  1 
2R_5039100_5039899_(800) (  344) GAGTGTGTGTAT  1 
X_17508500_17509199_(700 (    1) CTGTGTGTGAGC  1 
2L_5413600_5414399_(800) (  451) GAGTGCGTGCGC  1 
3R_25386700_25387599_(90 (  697) GAATGAGTGTGT  1 
3R_17378100_17378799_(70 (    4) GTGTGCGGGTGT  1 
2L_14472300_14473199_(90 (   30) GTGCGAGTGAGC  1 
2L_11434600_11435499_(90 (  161) GAGTGAGCGGGC  1 
//

Motif 3 position-specific scoring matrix

log-odds matrix: alength= 4 w= 12 n= 22570 bayes= 10.1534 E= 1.2e-026 
 -1177   -306    202  -1177 
   -19  -1177  -1177    156 
  -160  -1177    193  -1177 
 -1177   -306  -1177    190 
  -219  -1177    198  -1177 
    27    -48  -1177     98 
 -1177   -306    202  -1177 
 -1177   -106   -306    172 
 -1177  -1177    206  -1177 
    51   -148   -106     72 
  -219  -1177    198  -1177 
  -319     52  -1177    127

Motif 3 position-specific probability matrix

letter-probability matrix: alength= 4 w= 12 n= 22570 E= 1.2e-026 
 0.000075  0.028632  0.971219  0.000075 
 0.228581  0.000068  0.000068  0.771283 
 0.085764  0.000068  0.914093  0.000075 
 0.000075  0.028632  0.000068  0.971226 
 0.057201  0.000068  0.942656  0.000075 
 0.314270  0.171448  0.000068  0.514213 
 0.000075  0.028632  0.971219  0.000075 
 0.000075  0.114321  0.028632  0.856973 
 0.000075  0.000068  0.999783  0.000075 
 0.371397  0.085758  0.114321  0.428524 
 0.057201  0.000068  0.942656  0.000075 
 0.028638  0.342828  0.000068  0.628466






Time 1770.88 secs.

P N
MOTIF 4 width = 12 sites = 34 llr = 360 E-value = 3.4e-010

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	:	:	:	:	2	:	:	:	:	:	:
				pos.-specific	C	:	:	:	3	1	:	:	:	:	5	1	1
				probability	G	:	:	3	:	:	3	:	:	6	1	:	3
				matrix	T	a	a	7	7	9	5	a	a	4	4	9	6
.
				bits	2.1
					1.9
					1.7
					1.4
				Information	1.2
				content	1.0
				(15.3 bits)	0.8
					0.6
					0.4
					0.2
					0.0
.
				Multilevel		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`G`	`C`	`T`	`T`
				consensus				`G`	`C`		`G`			`T`	`T`		`G`
				sequence							`A`

.

X_13798600_13799299_(700	-	68	1.74e-07	`TTTGGCCTTT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`G`	`T`	`T`	`T`	`GACTTTTTTT`
2L_20746400_20747199_(80	-	235	2.65e-07	`GGGGGTAGTA`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`AGGCCACTAA`
X_14247600_14248299_(700	-	563	2.65e-07	`TAATCATATG`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`TAATTTAAAA`
X_10896100_10896799_(700	+	137	6.01e-07	`AATTTAATTG`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`TCTGGTGAGG`
X_13798600_13799299_(700	+	660	6.01e-07	`ATCAGACCAG`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`CGAAAATGCG`
3R_21504100_21504899_(80	+	51	6.01e-07	`TTCATTAAAC`		`T`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`G`	`C`	`T`	`T`	`ATATAAATGC`
2R_14356700_14357399_(70	+	632	8.44e-07	`TCTCTGTACG`		`T`	`T`	`G`	`T`	`T`	`T`	`T`	`T`	`G`	`C`	`T`	`T`	`CGGTTTGGTT`
X_13798600_13799299_(700	-	136	8.44e-07	`GTGTGTGTTT`		`T`	`T`	`G`	`T`	`T`	`T`	`T`	`T`	`G`	`C`	`T`	`T`	`GCTCTGTGTT`
X_14247600_14248299_(700	+	248	1.25e-06	`GCTGTCTCTA`		`T`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`G`	`T`	`T`	`T`	`CTGCCTCGGC`
X_17098500_17099199_(700	+	267	1.85e-06	`AATTGTTAAT`		`T`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`G`	`C`	`T`	`G`	`GCCTTAAGAA`
X_8717700_8718299_(600)	-	327	3.12e-06	`GCGCTACTCT`		`T`	`T`	`G`	`T`	`T`	`T`	`T`	`T`	`G`	`T`	`T`	`G`	`TCGCTGTTTG`
2L_11434600_11435499_(90	+	797	3.12e-06	`ATCAAAATGA`		`T`	`T`	`T`	`C`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`TGGCTTTCTG`
3R_14525400_14526099_(70	-	26	4.03e-06	`TGTCGCGTGT`		`T`	`T`	`T`	`C`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`G`	`TCAACATCAA`
2L_14472300_14473199_(90	-	359	5.63e-06	`GCTCAGTGAG`		`T`	`T`	`G`	`T`	`T`	`G`	`T`	`T`	`G`	`T`	`T`	`G`	`TGGCTGCTTT`
2R_6957200_6957899_(700)	-	83	6.76e-06	`AGAAAGCACG`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`C`	`GGTTAATGAG`
X_13798600_13799299_(700	-	175	6.76e-06	`CGTCGCATGT`		`T`	`T`	`G`	`T`	`T`	`A`	`T`	`T`	`G`	`T`	`T`	`G`	`CCGCCTTGCC`
2L_14472300_14473199_(90	-	790	7.63e-06	`AGGTTTCTTA`		`T`	`T`	`T`	`T`	`T`	`G`	`T`	`T`	`G`	`G`	`T`	`T`	`ATATCTCTTG`
3L_1107600_1108399_(800)	-	377	8.37e-06	`GGCCGGGTCA`		`T`	`T`	`G`	`T`	`T`	`G`	`T`	`T`	`T`	`T`	`T`	`G`	`CGCACATGGC`
3R_21504100_21504899_(80	+	189	9.28e-06	`CTTTTTATAA`		`T`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`G`	`G`	`T`	`T`	`TTTTTTCCAG`
2R_14030000_14030899_(90	-	391	1.00e-05	`TTGCTCCATG`		`T`	`T`	`G`	`C`	`T`	`G`	`T`	`T`	`G`	`C`	`T`	`G`	`CTGCTGCATC`
3R_17378100_17378799_(70	+	686	1.00e-05	`GTTGGTTTTG`		`T`	`T`	`G`	`C`	`T`	`G`	`T`	`T`	`G`	`C`	`T`	`G`	`TGG`
2R_6957200_6957899_(700)	+	386	1.10e-05	`GCCCCTCTCT`		`T`	`T`	`T`	`T`	`C`	`A`	`T`	`T`	`T`	`C`	`T`	`T`	`TCCAATTACC`
2R_8758700_8759399_(700)	-	674	1.21e-05	`CCATAATGTA`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`C`	`G`	`CCATAATGCT`
2L_11434600_11435499_(90	+	606	1.30e-05	`GTTATGAGCG`		`T`	`T`	`G`	`T`	`T`	`G`	`T`	`T`	`G`	`C`	`C`	`T`	`TTTTTAATTT`
3R_22366000_22366799_(80	+	676	1.52e-05	`TTCTTCTTAT`		`T`	`T`	`T`	`C`	`T`	`T`	`T`	`T`	`T`	`C`	`T`	`C`	`CTCGTCGCTT`
X_13798600_13799299_(700	-	116	1.52e-05	`TTGCTCTGTG`		`T`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`T`	`C`	`T`	`T`	`TCTTTTACTG`
2L_20746400_20747199_(80	+	297	1.65e-05	`TCGCCGCATC`		`T`	`T`	`T`	`C`	`T`	`A`	`T`	`T`	`G`	`C`	`C`	`T`	`GACTTGGCGT`
2R_8758700_8759399_(700)	-	202	1.77e-05	`CACCCGCTCG`		`T`	`T`	`T`	`T`	`C`	`G`	`T`	`T`	`T`	`T`	`T`	`G`	`GTAATGAAAT`
2L_20746400_20747199_(80	+	26	1.77e-05	`TATAGTTAAC`		`T`	`T`	`T`	`C`	`C`	`T`	`T`	`T`	`G`	`T`	`T`	`G`	`CCTCTAATGC`
X_3050400_3051099_(700)	+	9	1.88e-05	`TGGATCGC`		`T`	`T`	`T`	`G`	`T`	`T`	`T`	`T`	`G`	`T`	`T`	`T`	`GGCGCCGTCT`
X_13798600_13799299_(700	-	52	2.04e-05	`TTGTTTGACT`		`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`G`	`C`	`C`	`C`	`ATTTCCTTTC`
2L_11434600_11435499_(90	+	850	2.46e-05	`CTTTAATTAT`		`T`	`T`	`T`	`T`	`C`	`G`	`T`	`T`	`G`	`C`	`C`	`T`	`CTCTGCAAAT`
2R_8758700_8759399_(700)	+	500	2.61e-05	`CCCGGCATAT`		`T`	`T`	`T`	`C`	`C`	`A`	`T`	`T`	`T`	`T`	`T`	`T`	`TTCGGCGCGG`
3R_17378100_17378799_(70	+	671	2.79e-05	`CGGCTCCTTG`		`T`	`T`	`G`	`C`	`T`	`G`	`T`	`T`	`G`	`G`	`T`	`T`	`TTGTTGCTGT`

Motif 4 block diagrams

Name

Lowest
p-value

Motifs

X_13798600_13799299_(700

2e-05

-4

2L_20746400_20747199_(80

1.8e-05

-4

X_14247600_14248299_(700

1.2e-06

-4

X_10896100_10896799_(700

6e-07

3R_21504100_21504899_(80

9.3e-06

2R_14356700_14357399_(70

8.4e-07

X_17098500_17099199_(700

1.8e-06

X_8717700_8718299_(600)

3.1e-06

-4

2L_11434600_11435499_(90

2.5e-05

3R_14525400_14526099_(70

4e-06

-4

2L_14472300_14473199_(90

5.6e-06

-4

2R_6957200_6957899_(700)

1.1e-05

-4

3L_1107600_1108399_(800)

8.4e-06

-4

2R_14030000_14030899_(90

1e-05

-4

3R_17378100_17378799_(70

2.8e-05

2R_8758700_8759399_(700)

2.6e-05

-4

3R_22366000_22366799_(80

1.5e-05

X_3050400_3051099_(700)

1.9e-05

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

Motif 4 in BLOCKS format

BL   MOTIF 4 width=12 seqs=34
X_13798600_13799299_(700 (   68) TTTTTTTTGTTT  1 
2L_20746400_20747199_(80 (  235) TTTTTTTTTCTT  1 
X_14247600_14248299_(700 (  563) TTTTTTTTTCTT  1 
X_10896100_10896799_(700 (  137) TTTTTTTTTTTT  1 
X_13798600_13799299_(700 (  660) TTTTTTTTTTTT  1 
3R_21504100_21504899_(80 (   51) TTTTTATTGCTT  1 
2R_14356700_14357399_(70 (  632) TTGTTTTTGCTT  1 
X_13798600_13799299_(700 (  136) TTGTTTTTGCTT  1 
X_14247600_14248299_(700 (  248) TTTTTATTGTTT  1 
X_17098500_17099199_(700 (  267) TTTTTATTGCTG  1 
X_8717700_8718299_(600)  (  327) TTGTTTTTGTTG  1 
2L_11434600_11435499_(90 (  797) TTTCTTTTTTTT  1 
3R_14525400_14526099_(70 (   26) TTTCTTTTTCTG  1 
2L_14472300_14473199_(90 (  359) TTGTTGTTGTTG  1 
2R_6957200_6957899_(700) (   83) TTTTTTTTTCTC  1 
X_13798600_13799299_(700 (  175) TTGTTATTGTTG  1 
2L_14472300_14473199_(90 (  790) TTTTTGTTGGTT  1 
3L_1107600_1108399_(800) (  377) TTGTTGTTTTTG  1 
3R_21504100_21504899_(80 (  189) TTTTTATTGGTT  1 
2R_14030000_14030899_(90 (  391) TTGCTGTTGCTG  1 
3R_17378100_17378799_(70 (  686) TTGCTGTTGCTG  1 
2R_6957200_6957899_(700) (  386) TTTTCATTTCTT  1 
2R_8758700_8759399_(700) (  674) TTTTTTTTTTCG  1 
2L_11434600_11435499_(90 (  606) TTGTTGTTGCCT  1 
3R_22366000_22366799_(80 (  676) TTTCTTTTTCTC  1 
X_13798600_13799299_(700 (  116) TTTTTCTTTCTT  1 
2L_20746400_20747199_(80 (  297) TTTCTATTGCCT  1 
2R_8758700_8759399_(700) (  202) TTTTCGTTTTTG  1 
2L_20746400_20747199_(80 (   26) TTTCCTTTGTTG  1 
X_3050400_3051099_(700)  (    9) TTTGTTTTGTTT  1 
X_13798600_13799299_(700 (   52) TTTTTTTTGCCC  1 
2L_11434600_11435499_(90 (  850) TTTTCGTTGCCT  1 
2R_8758700_8759399_(700) (  500) TTTCCATTTTTT  1 
3R_17378100_17378799_(70 (  671) TTGCTGTTGGTT  1 
//

Motif 4 position-specific scoring matrix

log-odds matrix: alength= 4 w= 12 n= 22570 bayes= 8.91069 E= 3.4e-010 
 -1173  -1173  -1173    194 
 -1173  -1173  -1173    194 
 -1173  -1173     30    144 
 -1173     15   -302    144 
 -1173    -70  -1173    171 
   -15   -302     15     85 
 -1173  -1173  -1173    194 
 -1173  -1173  -1173    194 
 -1173  -1173    130     66 
 -1173    106   -144     66 
 -1173    -70  -1173    171 
 -1173   -144     44    117

Motif 4 position-specific probability matrix

letter-probability matrix: alength= 4 w= 12 n= 22570 E= 3.4e-010 
 0.000077  0.000070  0.000070  0.999783 
 0.000077  0.000070  0.000070  0.999783 
 0.000077  0.000070  0.294101  0.705751 
 0.000077  0.264698  0.029473  0.705751 
 0.000077  0.147086  0.000070  0.852767 
 0.235302  0.029473  0.264698  0.470527 
 0.000077  0.000070  0.000070  0.999783 
 0.000077  0.000070  0.000070  0.999783 
 0.000077  0.000070  0.588133  0.411720 
 0.000077  0.499923  0.088280  0.411720 
 0.000077  0.147086  0.000070  0.852767 
 0.000077  0.088280  0.323505  0.588139






Time 2337.13 secs.

P N
MOTIF 5 width = 11 sites = 23 llr = 258 E-value = 6.8e-006

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	:	3	:	:	9	:	1	3	:	:
				pos.-specific	C	:	8	:	:	8	:	:	8	:	:	a
				probability	G	a	:	5	9	2	1	a	:	7	a	:
				matrix	T	:	1	3	:	:	:	:	:	:	:	:
.
				bits	2.1
					1.9
					1.7
					1.4
				Information	1.2
				content	1.0
				(16.2 bits)	0.8
					0.6
					0.4
					0.2
					0.0
.
				Multilevel		`G`	`C`	`G`	`G`	`C`	`A`	`G`	`C`	`G`	`G`	`C`
				consensus				`A`						`A`
				sequence				`T`

.

2R_8758700_8759399_(700)	+	402	1.60e-07	`ATTGGCGGCT`		`G`	`C`	`G`	`G`	`C`	`A`	`G`	`C`	`G`	`G`	`C`	`ATCGTTGTCG`
3R_8837700_8838499_(800)	+	114	1.60e-07	`TCGAAAATCC`		`G`	`C`	`G`	`G`	`C`	`A`	`G`	`C`	`G`	`G`	`C`	`GATTTTTCCA`
2L_14472300_14473199_(90	-	222	1.60e-07	`TGCAGTGGTG`		`G`	`C`	`G`	`G`	`C`	`A`	`G`	`C`	`G`	`G`	`C`	`GCGGCAGAGG`
3R_25386700_25387599_(90	+	565	1.60e-07	`GACTGCGGCT`		`G`	`C`	`G`	`G`	`C`	`A`	`G`	`C`	`G`	`G`	`C`	`TGAGGCGCCG`
X_17980400_17981199_(800	+	256	5.08e-07	`AGTGACTGCG`		`G`	`C`	`T`	`G`	`C`	`A`	`G`	`C`	`G`	`G`	`C`	`GCTCGAAAAT`
2R_14030000_14030899_(90	+	369	5.08e-07	`TTTGCATGCA`		`G`	`C`	`A`	`G`	`C`	`A`	`G`	`C`	`G`	`G`	`C`	`AGATGCAGCA`
X_17980400_17981199_(800	-	179	1.22e-06	`AGCAGCAGCA`		`G`	`C`	`A`	`G`	`C`	`A`	`G`	`C`	`A`	`G`	`C`	`AAGCGATTGT`
2R_14030000_14030899_(90	-	157	1.22e-06	`CAAAACAACA`		`G`	`C`	`A`	`G`	`C`	`A`	`G`	`C`	`A`	`G`	`C`	`AGTAGCCGCC`
2L_14472300_14473199_(90	-	245	1.22e-06	`GGGGCTGTCA`		`G`	`C`	`A`	`G`	`C`	`A`	`G`	`C`	`A`	`G`	`C`	`GCTGCAGTGG`
2L_14472300_14473199_(90	-	211	1.72e-06	`CGGCAGCGGC`		`G`	`C`	`G`	`G`	`C`	`A`	`G`	`A`	`G`	`G`	`C`	`CTCATTGTCT`
3L_19484500_19485299_(80	-	447	2.06e-06	`CTTGGCGATG`		`G`	`C`	`T`	`G`	`G`	`A`	`G`	`C`	`G`	`G`	`C`	`TGAAATGGCC`
3L_19484500_19485299_(80	-	249	2.06e-06	`CTTGGCCACT`		`G`	`C`	`T`	`G`	`G`	`A`	`G`	`C`	`G`	`G`	`C`	`AATAGCCACA`
2R_14030000_14030899_(90	+	142	2.56e-06	`TGCTGCTATT`		`G`	`C`	`T`	`G`	`C`	`G`	`G`	`C`	`G`	`G`	`C`	`TACTGCTGCT`
3R_12589500_12590299_(80	+	357	3.64e-06	`TGGCGACGGA`		`G`	`C`	`T`	`G`	`C`	`A`	`G`	`A`	`G`	`G`	`C`	`AGCGACTGCG`
X_17508500_17509199_(700	+	73	5.25e-06	`CGCCTTCGCC`		`G`	`C`	`G`	`G`	`C`	`A`	`G`	`C`	`G`	`A`	`C`	`GGAGACAGCG`
3R_8837700_8838499_(800)	-	640	8.49e-06	`CGCACCAAAT`		`G`	`T`	`G`	`G`	`C`	`G`	`G`	`C`	`G`	`G`	`C`	`AAAACAACAA`
2R_14030000_14030899_(90	-	870	1.04e-05	`CAGCGATGAA`		`G`	`C`	`G`	`T`	`C`	`A`	`G`	`C`	`A`	`G`	`C`	`AACATGTGCT`
2R_5039100_5039899_(800)	-	183	1.20e-05	`CATCCACCCC`		`G`	`T`	`T`	`G`	`G`	`A`	`G`	`C`	`G`	`G`	`C`	`GGCAGGGGTG`
3L_19484500_19485299_(80	-	126	1.24e-05	`AGTTGCAACC`		`G`	`T`	`G`	`G`	`G`	`A`	`G`	`C`	`A`	`G`	`C`	`GTAAGTGGAC`
X_9717100_9717899_(800)	-	573	1.37e-05	`GGGGGGATCA`		`G`	`G`	`A`	`G`	`C`	`A`	`G`	`C`	`A`	`G`	`C`	`AGTCAGTGCT`
X_17508500_17509199_(700	-	510	1.54e-05	`GCGTGAAGGA`		`G`	`C`	`G`	`G`	`C`	`A`	`G`	`A`	`C`	`G`	`C`	`GCTCGCAATG`
2R_14030000_14030899_(90	-	127	1.54e-05	`CGCAGCAATA`		`G`	`C`	`A`	`G`	`C`	`A`	`G`	`T`	`A`	`G`	`C`	`AACGACTCAA`
2R_5039100_5039899_(800)	+	788	1.91e-05	`GCCGCTCCCA`		`G`	`C`	`G`	`A`	`C`	`G`	`G`	`C`	`G`	`G`	`C`	`CA`

Motif 5 block diagrams

Name

Lowest
p-value

Motifs

2R_8758700_8759399_(700)

1.6e-07

3R_8837700_8838499_(800)

8.5e-06

-5

2L_14472300_14473199_(90

1.2e-06

-5

3R_25386700_25387599_(90

1.6e-07

X_17980400_17981199_(800

5.1e-07

-5

2R_14030000_14030899_(90

1e-05

-5

3L_19484500_19485299_(80

1.2e-05

-5

3R_12589500_12590299_(80

3.6e-06

X_17508500_17509199_(700

1.5e-05

-5

2R_5039100_5039899_(800)

1.2e-05

-5

X_9717100_9717899_(800)

1.4e-05

-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

Motif 5 in BLOCKS format

BL   MOTIF 5 width=11 seqs=23
2R_8758700_8759399_(700) (  402) GCGGCAGCGGC  1 
3R_8837700_8838499_(800) (  114) GCGGCAGCGGC  1 
2L_14472300_14473199_(90 (  222) GCGGCAGCGGC  1 
3R_25386700_25387599_(90 (  565) GCGGCAGCGGC  1 
X_17980400_17981199_(800 (  256) GCTGCAGCGGC  1 
2R_14030000_14030899_(90 (  369) GCAGCAGCGGC  1 
X_17980400_17981199_(800 (  179) GCAGCAGCAGC  1 
2R_14030000_14030899_(90 (  157) GCAGCAGCAGC  1 
2L_14472300_14473199_(90 (  245) GCAGCAGCAGC  1 
2L_14472300_14473199_(90 (  211) GCGGCAGAGGC  1 
3L_19484500_19485299_(80 (  447) GCTGGAGCGGC  1 
3L_19484500_19485299_(80 (  249) GCTGGAGCGGC  1 
2R_14030000_14030899_(90 (  142) GCTGCGGCGGC  1 
3R_12589500_12590299_(80 (  357) GCTGCAGAGGC  1 
X_17508500_17509199_(700 (   73) GCGGCAGCGAC  1 
3R_8837700_8838499_(800) (  640) GTGGCGGCGGC  1 
2R_14030000_14030899_(90 (  870) GCGTCAGCAGC  1 
2R_5039100_5039899_(800) (  183) GTTGGAGCGGC  1 
3L_19484500_19485299_(80 (  126) GTGGGAGCAGC  1 
X_9717100_9717899_(800)  (  573) GGAGCAGCAGC  1 
X_17508500_17509199_(700 (  510) GCGGCAGACGC  1 
2R_14030000_14030899_(90 (  127) GCAGCAGTAGC  1 
2R_5039100_5039899_(800) (  788) GCGACGGCGGC  1 
//

Motif 5 position-specific scoring matrix

log-odds matrix: alength= 4 w= 11 n= 22600 bayes= 11.5001 E= 6.8e-006 
 -1117  -1117    206  -1117 
 -1117    179   -246   -100 
     0  -1117    100      0 
  -258  -1117    193   -258 
 -1117    179    -46  -1117 
   174  -1117    -87  -1117 
 -1117  -1117    206  -1117 
  -100    179  -1117   -258 
    22   -246    145  -1117 
  -258  -1117    200  -1117 
 -1117    206  -1117  -1117

Motif 5 position-specific probability matrix

letter-probability matrix: alength= 4 w= 11 n= 22600 E= 6.8e-006 
 0.000113  0.000104  0.999669  0.000113 
 0.000113  0.825832  0.043563  0.130491 
 0.260870  0.000104  0.478157  0.260870 
 0.043573  0.000104  0.912751  0.043573 
 0.000113  0.825832  0.173941  0.000113 
 0.869301  0.000104  0.130482  0.000113 
 0.000113  0.000104  0.999669  0.000113 
 0.130491  0.825832  0.000104  0.043573 
 0.304329  0.043563  0.651994  0.000113 
 0.043573  0.000104  0.956210  0.000113 
 0.000113  0.999669  0.000104  0.000113






Time 2892.46 secs.

P N
MOTIF 6 width = 11 sites = 26 llr = 274 E-value = 4.9e-002

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	:	a	:	:	3	:	:	4	5	3
				pos.-specific	C	8	a	:	7	a	:	a	a	5	2	7
				probability	G	2	:	:	1	:	7	:	:	1	:	:
				matrix	T	:	:	:	2	:	1	:	:	:	3	:
.
				bits	2.1
					1.9
					1.7
					1.4
				Information	1.2
				content	1.0
				(15.2 bits)	0.8
					0.6
					0.4
					0.2
					0.0
.
				Multilevel		`C`	`C`	`A`	`C`	`C`	`G`	`C`	`C`	`C`	`A`	`C`
				consensus							`A`			`A`	`T`	`A`
				sequence

.

X_17980400_17981199_(800	+	760	1.74e-07	`GCGTACCCAC`		`C`	`C`	`A`	`C`	`C`	`G`	`C`	`C`	`C`	`A`	`C`	`CGCCCATAGC`
X_17980400_17981199_(800	-	15	1.74e-07	`ACCACACACC`		`C`	`C`	`A`	`C`	`C`	`G`	`C`	`C`	`C`	`A`	`C`	`CACCCATTGC`
2R_14356700_14357399_(70	+	516	1.74e-07	`CACCACCCAC`		`C`	`C`	`A`	`C`	`C`	`G`	`C`	`C`	`C`	`A`	`C`	`TCAACCCCCT`
X_14247600_14248299_(700	+	391	1.74e-07	`GCCCCTCCGT`		`C`	`C`	`A`	`C`	`C`	`G`	`C`	`C`	`C`	`A`	`C`	`CGCCAACAAC`
2R_14356700_14357399_(70	+	505	1.11e-06	`CATCCCCCGA`		`C`	`C`	`A`	`C`	`C`	`A`	`C`	`C`	`C`	`A`	`C`	`CCACCGCCCA`
X_13798600_13799299_(700	+	360	1.11e-06	`CCACTGCCAC`		`C`	`C`	`A`	`C`	`C`	`A`	`C`	`C`	`C`	`A`	`C`	`CACGCCCCCT`
X_9717100_9717899_(800)	+	634	2.41e-06	`CCCACATTTT`		`C`	`C`	`A`	`C`	`C`	`A`	`C`	`C`	`C`	`T`	`C`	`CTGAAACTCA`
X_16943800_16944599_(800	-	443	3.01e-06	`GCTGGAATAG`		`C`	`C`	`A`	`C`	`C`	`G`	`C`	`C`	`A`	`T`	`A`	`GCCGCCAGTG`
X_8717700_8718299_(600)	+	190	5.68e-06	`CTTACTTCCT`		`C`	`C`	`A`	`T`	`C`	`G`	`C`	`C`	`C`	`T`	`C`	`ACACGCCATC`
3L_1107600_1108399_(800)	+	183	5.68e-06	`GAGTCCTGCT`		`G`	`C`	`A`	`C`	`C`	`G`	`C`	`C`	`C`	`A`	`A`	`CTGCACCACC`
X_16943800_16944599_(800	+	716	7.01e-06	`ATTCGGTGCA`		`C`	`C`	`A`	`C`	`C`	`A`	`C`	`C`	`A`	`C`	`C`	`ACTTGGCTTG`
2R_8758700_8759399_(700)	+	289	8.03e-06	`ATTGCCATCG`		`C`	`C`	`A`	`T`	`C`	`G`	`C`	`C`	`A`	`T`	`C`	`GCCATCGCAG`
3R_22366000_22366799_(80	-	428	8.03e-06	`GTTGTCACCG`		`C`	`C`	`A`	`T`	`C`	`G`	`C`	`C`	`A`	`T`	`C`	`CCGACTTCCC`
3L_1107600_1108399_(800)	+	96	8.03e-06	`ATCGTCGTCG`		`C`	`C`	`A`	`T`	`C`	`G`	`C`	`C`	`A`	`T`	`C`	`GTAGCTGTGT`
X_11044500_11045199_(700	+	451	8.82e-06	`AATGGAGGCA`		`C`	`C`	`A`	`C`	`C`	`G`	`C`	`C`	`G`	`A`	`A`	`CGGCAGAGGA`
X_16943800_16944599_(800	-	629	8.82e-06	`AAGGGCAGCA`		`C`	`C`	`A`	`C`	`C`	`G`	`C`	`C`	`G`	`A`	`A`	`GGAGCTTCCA`
X_8717700_8718299_(600)	-	526	1.21e-05	`CCTTTGCCGC`		`C`	`C`	`A`	`A`	`C`	`G`	`C`	`C`	`C`	`A`	`C`	`ATACTCCCGC`
3L_1107600_1108399_(800)	+	340	1.37e-05	`GTTGCCATGT`		`G`	`C`	`A`	`C`	`C`	`A`	`C`	`C`	`C`	`A`	`A`	`CTTTTCTTTG`
3L_1107600_1108399_(800)	+	196	1.37e-05	`CCGCCCAACT`		`G`	`C`	`A`	`C`	`C`	`A`	`C`	`C`	`C`	`A`	`A`	`CTGCGCCACC`
X_16943800_16944599_(800	-	470	1.56e-05	`TATGGCAGGC`		`G`	`C`	`A`	`G`	`C`	`G`	`C`	`C`	`C`	`A`	`C`	`AAAGCCGCTG`
X_16943800_16944599_(800	-	677	1.68e-05	`AAAGCCGCCG`		`C`	`C`	`A`	`G`	`C`	`G`	`C`	`C`	`A`	`T`	`A`	`GCCAGCGCCA`
X_16943800_16944599_(800	-	665	1.68e-05	`AGCGCCATAG`		`C`	`C`	`A`	`G`	`C`	`G`	`C`	`C`	`A`	`T`	`A`	`GCCGTAGGAG`
2L_11434600_11435499_(90	+	458	1.94e-05	`GAGGGGGCTT`		`C`	`C`	`C`	`C`	`C`	`G`	`C`	`C`	`A`	`A`	`C`	`GAGCCCTTGG`
3L_6076100_6076799_(700)	+	293	2.25e-05	`CCGCACCGCA`		`C`	`C`	`A`	`C`	`C`	`T`	`C`	`C`	`A`	`C`	`C`	`TCTACCCACT`
3L_6076100_6076799_(700)	+	274	2.47e-05	`CAGTGTGCTG`		`G`	`C`	`A`	`C`	`C`	`A`	`C`	`C`	`A`	`C`	`C`	`GCACCGCACC`
2R_8758700_8759399_(700)	-	3	2.65e-05	`CGAGTGTCCT`		`C`	`C`	`A`	`C`	`C`	`T`	`C`	`C`	`C`	`C`	`A`	`TC`

Motif 6 block diagrams

Name

Lowest
p-value

Motifs

X_17980400_17981199_(800

1.7e-07

-6

2R_14356700_14357399_(70

1.1e-06

X_14247600_14248299_(700

1.7e-07

X_13798600_13799299_(700

1.1e-06

X_9717100_9717899_(800)

2.4e-06

X_16943800_16944599_(800

1.7e-05

-6

X_8717700_8718299_(600)

1.2e-05

-6

3L_1107600_1108399_(800)

1.4e-05

2R_8758700_8759399_(700)

2.6e-05

-6

3R_22366000_22366799_(80

8e-06

-6

X_11044500_11045199_(700

8.8e-06

2L_11434600_11435499_(90

1.9e-05

3L_6076100_6076799_(700)

2.3e-05

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

Motif 6 in BLOCKS format

BL   MOTIF 6 width=11 seqs=26
X_17980400_17981199_(800 (  760) CCACCGCCCAC  1 
X_17980400_17981199_(800 (   15) CCACCGCCCAC  1 
2R_14356700_14357399_(70 (  516) CCACCGCCCAC  1 
X_14247600_14248299_(700 (  391) CCACCGCCCAC  1 
2R_14356700_14357399_(70 (  505) CCACCACCCAC  1 
X_13798600_13799299_(700 (  360) CCACCACCCAC  1 
X_9717100_9717899_(800)  (  634) CCACCACCCTC  1 
X_16943800_16944599_(800 (  443) CCACCGCCATA  1 
X_8717700_8718299_(600)  (  190) CCATCGCCCTC  1 
3L_1107600_1108399_(800) (  183) GCACCGCCCAA  1 
X_16943800_16944599_(800 (  716) CCACCACCACC  1 
2R_8758700_8759399_(700) (  289) CCATCGCCATC  1 
3R_22366000_22366799_(80 (  428) CCATCGCCATC  1 
3L_1107600_1108399_(800) (   96) CCATCGCCATC  1 
X_11044500_11045199_(700 (  451) CCACCGCCGAA  1 
X_16943800_16944599_(800 (  629) CCACCGCCGAA  1 
X_8717700_8718299_(600)  (  526) CCAACGCCCAC  1 
3L_1107600_1108399_(800) (  340) GCACCACCCAA  1 
3L_1107600_1108399_(800) (  196) GCACCACCCAA  1 
X_16943800_16944599_(800 (  470) GCAGCGCCCAC  1 
X_16943800_16944599_(800 (  677) CCAGCGCCATA  1 
X_16943800_16944599_(800 (  665) CCAGCGCCATA  1 
2L_11434600_11435499_(90 (  458) CCCCCGCCAAC  1 
3L_6076100_6076799_(700) (  293) CCACCTCCACC  1 
3L_6076100_6076799_(700) (  274) GCACCACCACC  1 
2R_8758700_8759399_(700) (    3) CCACCTCCCCA  1 
//

Motif 6 position-specific scoring matrix

log-odds matrix: alength= 4 w= 11 n= 22600 bayes= 11.3931 E= 4.9e-002 
 -1134    176    -31  -1134 
 -1134    206  -1134  -1134 
   188   -263  -1134  -1134 
  -276    153   -105    -76 
 -1134    206  -1134  -1134 
     5  -1134    145   -176 
 -1134    206  -1134  -1134 
 -1134    206  -1134  -1134 
    56    117   -164  -1134 
   105    -64  -1134     24 
    41    145  -1134  -1134

Motif 6 position-specific probability matrix

letter-probability matrix: alength= 4 w= 11 n= 22600 E= 4.9e-002 
 0.000100  0.807474  0.192326  0.000100 
 0.000100  0.999707  0.000092  0.000100 
 0.961269  0.038539  0.000092  0.000100 
 0.038547  0.692133  0.115432  0.153887 
 0.000100  0.999707  0.000092  0.000100 
 0.269228  0.000092  0.653687  0.076994 
 0.000100  0.999707  0.000092  0.000100 
 0.000100  0.999707  0.000092  0.000100 
 0.384568  0.538346  0.076985  0.000100 
 0.538355  0.153879  0.000092  0.307674 
 0.346121  0.653687  0.000092  0.000100






Time 3440.34 secs.

P N
MOTIF 7 width = 11 sites = 30 llr = 314 E-value = 4.7e-006

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	1	1	:	:	:	:	:	:	:	:	:
				pos.-specific	C	6	1	a	2	a	:	9	:	8	:	9
				probability	G	2	:	:	:	:	5	:	:	:	8	1
				matrix	T	1	8	:	8	:	5	1	a	2	2	:
.
				bits	2.1
					1.9
					1.7
					1.4
				Information	1.2
				content	1.0
				(15.1 bits)	0.8
					0.6
					0.4
					0.2
					0.0
.
				Multilevel		`C`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`C`	`G`	`C`
				consensus		`G`					`G`			`T`	`T`
				sequence

.

X_17508500_17509199_(700	+	405	3.97e-07	`GGTTATGTGC`		`C`	`T`	`C`	`T`	`C`	`G`	`C`	`T`	`C`	`G`	`C`	`ACGCTCGACA`
2L_20746400_20747199_(80	+	429	7.94e-07	`CCTCGCCTCC`		`G`	`T`	`C`	`T`	`C`	`G`	`C`	`T`	`C`	`G`	`C`	`TCACTCGCTC`
X_8717700_8718299_(600)	+	224	1.66e-06	`CTCTCTCTCT`		`C`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`C`	`TCGATAATTA`
2R_14356700_14357399_(70	+	236	1.66e-06	`CTCTCTCTCT`		`C`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`T`	`G`	`C`	`GCTCTCTCCC`
X_13798600_13799299_(700	-	259	1.66e-06	`CCAACTCTTG`		`C`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`T`	`G`	`C`	`TTGCTCGCTC`
X_8717700_8718299_(600)	-	512	2.02e-06	`CGCCCACATA`		`C`	`T`	`C`	`C`	`C`	`G`	`C`	`T`	`C`	`G`	`C`	`CCCGTCTCTG`
X_9717100_9717899_(800)	-	384	2.02e-06	`ATGTCTCTAT`		`C`	`T`	`C`	`C`	`C`	`T`	`C`	`T`	`C`	`G`	`C`	`CTTCACTCAC`
2L_14472300_14473199_(90	+	568	3.29e-06	`CGCACAGTGC`		`A`	`T`	`C`	`T`	`C`	`G`	`C`	`T`	`C`	`G`	`C`	`ATGCAGCAGG`
2L_5413600_5414399_(800)	-	49	3.29e-06	`TTATTTGCGC`		`T`	`T`	`C`	`T`	`C`	`G`	`C`	`T`	`C`	`G`	`C`	`TGATTATTTC`
3R_12589500_12590299_(80	-	244	3.72e-06	`TTGTTTGGTG`		`C`	`T`	`C`	`T`	`C`	`T`	`T`	`T`	`C`	`G`	`C`	`CTTGCTCTTT`
X_17508500_17509199_(700	+	160	4.59e-06	`ACATACGGTT`		`G`	`T`	`C`	`T`	`C`	`G`	`C`	`T`	`C`	`T`	`C`	`GCGGCAAAAT`
2R_5039100_5039899_(800)	+	744	4.95e-06	`CGCTCAGGCT`		`G`	`T`	`C`	`C`	`C`	`G`	`C`	`T`	`C`	`G`	`C`	`ACCTGCCTGG`
2R_5039100_5039899_(800)	+	455	4.95e-06	`GGGCCCGCCC`		`G`	`T`	`C`	`C`	`C`	`G`	`C`	`T`	`C`	`G`	`C`	`TCCTGCGGAG`
2L_5413600_5414399_(800)	-	303	4.95e-06	`GACTCGCCCC`		`G`	`T`	`C`	`C`	`C`	`G`	`C`	`T`	`C`	`G`	`C`	`TCACGCATCC`
3L_6076100_6076799_(700)	+	429	5.79e-06	`CTCTCTCTCT`		`C`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`T`	`T`	`C`	`GATTGTTTGT`
X_13798600_13799299_(700	-	217	5.79e-06	`CTCTCTCTCT`		`C`	`C`	`C`	`T`	`C`	`T`	`C`	`T`	`C`	`G`	`C`	`GTTCGCTTTG`
X_8717700_8718299_(600)	+	571	6.18e-06	`ACGATACGGC`		`C`	`A`	`C`	`T`	`C`	`G`	`C`	`T`	`C`	`G`	`C`	`TTGCTCGCTC`
2R_14356700_14357399_(70	+	326	7.81e-06	`GCCATTACGT`		`G`	`T`	`C`	`T`	`C`	`T`	`T`	`T`	`C`	`G`	`C`	`ACTCGCACTG`
2R_6957200_6957899_(700)	+	101	1.06e-05	`AAAACGTGCT`		`T`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`T`	`G`	`C`	`CTTTGTCATG`
X_17098500_17099199_(700	+	212	1.06e-05	`CTCTCTCTCT`		`C`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`G`	`AACTTAAGGG`
X_17098500_17099199_(700	-	164	1.06e-05	`TCGTTTGAGT`		`A`	`T`	`C`	`T`	`C`	`G`	`C`	`T`	`T`	`G`	`C`	`CGCCGTTTTC`
3R_17378100_17378799_(70	+	246	1.06e-05	`CTCTCTCTCT`		`C`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`C`	`T`	`G`	`CCTTTTAAGT`
3R_12589500_12590299_(80	-	123	1.06e-05	`CTATGAAAAG`		`C`	`T`	`C`	`T`	`C`	`G`	`C`	`T`	`T`	`G`	`G`	`GACTCTCTCT`
2L_14472300_14473199_(90	+	646	1.19e-05	`CGCCGGAGAG`		`C`	`G`	`C`	`T`	`C`	`T`	`C`	`T`	`C`	`G`	`C`	`GAGTGAGCGA`
3R_17378100_17378799_(70	-	25	1.19e-05	`TCCGCTCTGT`		`C`	`T`	`C`	`T`	`C`	`T`	`T`	`T`	`C`	`T`	`C`	`TGCATTTGGG`
X_17508500_17509199_(700	-	192	1.39e-05	`CCCGCGTACT`		`G`	`C`	`C`	`T`	`C`	`T`	`C`	`T`	`C`	`G`	`C`	`CATGAGTGGC`
3R_12589500_12590299_(80	+	414	1.68e-05	`ACGGTTAGCC`		`T`	`T`	`C`	`T`	`C`	`G`	`C`	`T`	`C`	`G`	`G`	`ATCGCTCTCG`
3R_25386700_25387599_(90	+	866	1.89e-05	`CCGTACAGCC`		`A`	`T`	`C`	`T`	`C`	`T`	`T`	`T`	`C`	`G`	`C`	`ACACTCGAAC`
X_17508500_17509199_(700	+	564	1.98e-05	`CCCACTGGCC`		`C`	`A`	`C`	`T`	`C`	`G`	`C`	`T`	`C`	`T`	`C`	`TGCCGAGAAA`
3R_8837700_8838499_(800)	-	692	3.71e-05	`CCCTCCCACC`		`C`	`T`	`T`	`T`	`C`	`T`	`C`	`T`	`T`	`G`	`C`	`ACTCGCGCTA`

Motif 7 block diagrams

Name

Lowest
p-value

Motifs

X_17508500_17509199_(700

1.4e-05

-7

2L_20746400_20747199_(80

7.9e-07

X_8717700_8718299_(600)

6.2e-06

-7

2R_14356700_14357399_(70

7.8e-06

X_13798600_13799299_(700

5.8e-06

-7

X_9717100_9717899_(800)

2e-06

-7

2L_14472300_14473199_(90

3.3e-06

2L_5413600_5414399_(800)

5e-06

-7

3R_12589500_12590299_(80

1.7e-05

-7

2R_5039100_5039899_(800)

5e-06

3L_6076100_6076799_(700)

5.8e-06

2R_6957200_6957899_(700)

1.1e-05

X_17098500_17099199_(700

1.1e-05

-7

3R_17378100_17378799_(70

1.1e-05

-7

3R_25386700_25387599_(90

1.9e-05

3R_8837700_8838499_(800)

3.7e-05

-7

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

Motif 7 in BLOCKS format

BL   MOTIF 7 width=11 seqs=30
X_17508500_17509199_(700 (  405) CTCTCGCTCGC  1 
2L_20746400_20747199_(80 (  429) GTCTCGCTCGC  1 
X_8717700_8718299_(600)  (  224) CTCTCTCTCTC  1 
2R_14356700_14357399_(70 (  236) CTCTCTCTTGC  1 
X_13798600_13799299_(700 (  259) CTCTCTCTTGC  1 
X_8717700_8718299_(600)  (  512) CTCCCGCTCGC  1 
X_9717100_9717899_(800)  (  384) CTCCCTCTCGC  1 
2L_14472300_14473199_(90 (  568) ATCTCGCTCGC  1 
2L_5413600_5414399_(800) (   49) TTCTCGCTCGC  1 
3R_12589500_12590299_(80 (  244) CTCTCTTTCGC  1 
X_17508500_17509199_(700 (  160) GTCTCGCTCTC  1 
2R_5039100_5039899_(800) (  744) GTCCCGCTCGC  1 
2R_5039100_5039899_(800) (  455) GTCCCGCTCGC  1 
2L_5413600_5414399_(800) (  303) GTCCCGCTCGC  1 
3L_6076100_6076799_(700) (  429) CTCTCTCTTTC  1 
X_13798600_13799299_(700 (  217) CCCTCTCTCGC  1 
X_8717700_8718299_(600)  (  571) CACTCGCTCGC  1 
2R_14356700_14357399_(70 (  326) GTCTCTTTCGC  1 
2R_6957200_6957899_(700) (  101) TTCTCTCTTGC  1 
X_17098500_17099199_(700 (  212) CTCTCTCTCTG  1 
X_17098500_17099199_(700 (  164) ATCTCGCTTGC  1 
3R_17378100_17378799_(70 (  246) CTCTCTCTCTG  1 
3R_12589500_12590299_(80 (  123) CTCTCGCTTGG  1 
2L_14472300_14473199_(90 (  646) CGCTCTCTCGC  1 
3R_17378100_17378799_(70 (   25) CTCTCTTTCTC  1 
X_17508500_17509199_(700 (  192) GCCTCTCTCGC  1 
3R_12589500_12590299_(80 (  414) TTCTCGCTCGG  1 
3R_25386700_25387599_(90 (  866) ATCTCTTTCGC  1 
X_17508500_17509199_(700 (  564) CACTCGCTCTC  1 
3R_8837700_8838499_(800) (  692) CTTTCTCTTGC  1 
//

Motif 7 position-specific scoring matrix

log-odds matrix: alength= 4 w= 11 n= 22600 bayes= 11.2618 E= 4.7e-006 
  -138    124     -4   -138 
  -197   -184   -284    168 
 -1155    201  -1155   -296 
 -1155    -52  -1155    168 
 -1155    206  -1155  -1155 
 -1155  -1155     96    103 
 -1155    186  -1155    -97 
 -1155  -1155  -1155    194 
 -1155    168  -1155    -16 
 -1155  -1155    168    -16 
 -1155    186    -84  -1155

Motif 7 position-specific probability matrix

letter-probability matrix: alength= 4 w= 11 n= 22600 E= 4.7e-006 
 0.100054  0.566558  0.233335  0.100054 
 0.066731  0.066724  0.033402  0.833143 
 0.000087  0.966424  0.000080  0.033409 
 0.000087  0.166691  0.000080  0.833143 
 0.000087  0.999746  0.000080  0.000087 
 0.000087  0.000080  0.466591  0.533243 
 0.000087  0.866458  0.000080  0.133376 
 0.000087  0.000080  0.000080  0.999754 
 0.000087  0.766491  0.000080  0.233343 
 0.000087  0.000080  0.766491  0.233343 
 0.000087  0.866458  0.133369  0.000087






Time 3982.17 secs.

P N
MOTIF 8 width = 8 sites = 16 llr = 176 E-value = 3.1e-001

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	:	:	a	:	a	a	a
				pos.-specific	C	:	a	a	:	:	:	:	:
				probability	G	a	:	:	:	:	:	:	:
				matrix	T	:	:	:	:	a	:	:	:
.
				bits	2.1
					1.9
					1.7
					1.4
				Information	1.2
				content	1.0
				(15.9 bits)	0.8
					0.6
					0.4
					0.2
					0.0
.
				Multilevel		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`
				consensus
				sequence

.

X_3050400_3051099_(700)	+	257	1.65e-05	`TCTCGCTTTA`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`TCATGCTGAA`
X_3050400_3051099_(700)	-	170	1.65e-05	`ACACATATTA`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`TCTGTATAAC`
X_3050400_3051099_(700)	-	145	1.65e-05	`AACACTCGCG`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`TCAATATTGA`
X_3050400_3051099_(700)	-	77	1.65e-05	`ACTACAGTTA`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`AGTCAAGAAA`
2R_8758700_8759399_(700)	-	432	1.65e-05	`GACAAATGCG`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`CAAAAATGGC`
X_8717700_8718299_(600)	+	298	1.65e-05	`ACAAATGATT`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`TTTGATGGCA`
X_8717700_8718299_(600)	+	79	1.65e-05	`GATAATTAAT`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`ATCGTTTATT`
X_10896100_10896799_(700	-	361	1.65e-05	`CCATGTGATG`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`ACGATCCAAT`
2L_20746400_20747199_(80	+	475	1.65e-05	`CTCCGTTTGA`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`TAAAGCGAGC`
2L_20746400_20747199_(80	-	320	1.65e-05	`TGCCATTAAA`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`TACGCCAAGT`
2L_20746400_20747199_(80	+	161	1.65e-05	`AAATCATATA`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`CTTTATTGCG`
2R_14030000_14030899_(90	+	470	1.65e-05	`CCTGTCGTTG`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`CGCCCGCTGG`
X_17098500_17099199_(700	+	369	1.65e-05	`ATAATTTGTA`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`TCTTTTAATC`
3R_21504100_21504899_(80	+	680	1.65e-05	`TAAAGGCCGG`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`AACAGAAGCC`
3R_21504100_21504899_(80	+	502	1.65e-05	`ACATTAAGTG`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`GGCAGCCGAA`
3R_12589500_12590299_(80	-	608	1.65e-05	`CCGAAAATGA`		`G`	`C`	`C`	`A`	`T`	`A`	`A`	`A`	`ACCCCAGTGC`

Motif 8 block diagrams

Name

Lowest
p-value

Motifs

X_3050400_3051099_(700)

1.7e-05

-8

2R_8758700_8759399_(700)

1.7e-05

-8

X_8717700_8718299_(600)

1.7e-05

X_10896100_10896799_(700

1.7e-05

-8

2L_20746400_20747199_(80

1.7e-05

-8

2R_14030000_14030899_(90

1.7e-05

X_17098500_17099199_(700

1.7e-05

3R_21504100_21504899_(80

1.7e-05

3R_12589500_12590299_(80

1.7e-05

-8

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

Motif 8 in BLOCKS format

BL   MOTIF 8 width=8 seqs=16
X_3050400_3051099_(700)  (  257) GCCATAAA  1 
X_3050400_3051099_(700)  (  170) GCCATAAA  1 
X_3050400_3051099_(700)  (  145) GCCATAAA  1 
X_3050400_3051099_(700)  (   77) GCCATAAA  1 
2R_8758700_8759399_(700) (  432) GCCATAAA  1 
X_8717700_8718299_(600)  (  298) GCCATAAA  1 
X_8717700_8718299_(600)  (   79) GCCATAAA  1 
X_10896100_10896799_(700 (  361) GCCATAAA  1 
2L_20746400_20747199_(80 (  475) GCCATAAA  1 
2L_20746400_20747199_(80 (  320) GCCATAAA  1 
2L_20746400_20747199_(80 (  161) GCCATAAA  1 
2R_14030000_14030899_(90 (  470) GCCATAAA  1 
X_17098500_17099199_(700 (  369) GCCATAAA  1 
3R_21504100_21504899_(80 (  680) GCCATAAA  1 
3R_21504100_21504899_(80 (  502) GCCATAAA  1 
3R_12589500_12590299_(80 (  608) GCCATAAA  1 
//

Motif 8 position-specific scoring matrix

log-odds matrix: alength= 4 w= 8 n= 22690 bayes= 10.4688 E= 3.1e-001 
 -1064  -1064    206  -1064 
 -1064    206  -1064  -1064 
 -1064    206  -1064  -1064 
   194  -1064  -1064  -1064 
 -1064  -1064  -1064    194 
   194  -1064  -1064  -1064 
   194  -1064  -1064  -1064 
   194  -1064  -1064  -1064

Motif 8 position-specific probability matrix

letter-probability matrix: alength= 4 w= 8 n= 22690 E= 3.1e-001 
 0.000163  0.000149  0.999525  0.000163 
 0.000163  0.999525  0.000149  0.000163 
 0.000163  0.999525  0.000149  0.000163 
 0.999538  0.000149  0.000149  0.000163 
 0.000163  0.000149  0.000149  0.999538 
 0.999538  0.000149  0.000149  0.000163 
 0.999538  0.000149  0.000149  0.000163 
 0.999538  0.000149  0.000149  0.000163






Time 4515.10 secs.

P N
MOTIF 9 width = 12 sites = 27 llr = 270 E-value = 2.7e+005

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	:	4	7	6	:	:	:	:	6	:	1
				pos.-specific	C	:	:	2	:	:	:	:	:	:	2	:	:
				probability	G	:	1	3	:	1	:	:	:	2	:	:	:
				matrix	T	9	9	1	2	3	a	a	a	8	1	a	9
.
				bits	2.1
					1.9
					1.7
					1.4
				Information	1.2
				content	1.0
				(14.4 bits)	0.8
					0.6
					0.4
					0.2
					0.0
.
				Multilevel		`T`	`T`	`A`	`A`	`A`	`T`	`T`	`T`	`T`	`A`	`T`	`T`
				consensus				`G`	`T`	`T`
				sequence				`C`

.

2L_5413600_5414399_(800)	-	65	9.92e-08	`CTGATTAATA`		`T`	`T`	`A`	`A`	`A`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`TGCGCTTCTC`
3R_14525400_14526099_(70	+	480	6.62e-07	`TCGTCTTAAT`		`T`	`T`	`T`	`A`	`A`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`GATATTATTC`
X_17098500_17099199_(700	-	396	1.12e-06	`AGCTCCGAAA`		`T`	`T`	`G`	`T`	`A`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`TGGTGTTTAG`
X_17508500_17509199_(700	-	16	1.49e-06	`TTGAAGAGTT`		`T`	`T`	`C`	`A`	`A`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`CAACTGTGTG`
X_3050400_3051099_(700)	+	623	1.94e-06	`AACACTTAAC`		`T`	`T`	`C`	`A`	`A`	`T`	`T`	`T`	`G`	`A`	`T`	`T`	`CGAAGTGCAT`
3R_14525400_14526099_(70	+	139	2.55e-06	`TCCCAGGGGT`		`T`	`T`	`C`	`A`	`G`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`TTTGTCCGTA`
3R_8837700_8838499_(800)	+	514	5.00e-06	`TCTTTGTAAT`		`T`	`T`	`A`	`T`	`A`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`CCGCCCGCCT`
X_17508500_17509199_(700	-	249	5.43e-06	`CAACAACCAC`		`T`	`T`	`A`	`A`	`T`	`T`	`T`	`T`	`T`	`A`	`T`	`A`	`TGTGCCGTTT`
2L_14472300_14473199_(90	+	92	5.43e-06	`GACAAACAAA`		`T`	`T`	`A`	`A`	`T`	`T`	`T`	`T`	`T`	`A`	`T`	`A`	`TGACATTAAA`
2R_14030000_14030899_(90	+	9	5.96e-06	`TACGGTTG`		`T`	`T`	`A`	`A`	`A`	`T`	`T`	`T`	`T`	`G`	`T`	`T`	`TATAAATCAG`
3R_14525400_14526099_(70	+	519	6.40e-06	`GCAGATTCCA`		`T`	`T`	`A`	`G`	`A`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`GCCCACCCAT`
X_13798600_13799299_(700	+	632	7.18e-06	`CCTATAAAAT`		`T`	`G`	`C`	`A`	`T`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`GTTATTATCA`
X_9717100_9717899_(800)	-	777	7.18e-06	`TGTTAGTTAG`		`T`	`T`	`A`	`A`	`T`	`T`	`T`	`T`	`G`	`C`	`T`	`T`	`TAAGCTCATG`
X_16943800_16944599_(800	+	783	8.92e-06	`CGTCAAGTGG`		`T`	`T`	`A`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`GATAAT`
3L_6076100_6076799_(700)	-	173	9.62e-06	`ATAGGAGTTA`		`T`	`T`	`G`	`A`	`T`	`T`	`T`	`T`	`G`	`C`	`T`	`T`	`GGCAACTGGT`
X_10896100_10896799_(700	+	124	1.07e-05	`GTGTTTACAC`		`T`	`T`	`G`	`A`	`A`	`T`	`T`	`T`	`A`	`A`	`T`	`T`	`GTTTTTTTTT`
3R_25386700_25387599_(90	-	43	1.15e-05	`CTCCGTGTTG`		`G`	`T`	`G`	`A`	`A`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`GTCTCCACTT`
X_13798600_13799299_(700	+	582	1.38e-05	`TAATGGAATA`		`T`	`T`	`T`	`A`	`G`	`T`	`T`	`T`	`T`	`C`	`T`	`T`	`AAAATATCAA`
2L_11434600_11435499_(90	+	122	1.62e-05	`CGCTCTCATC`		`A`	`T`	`A`	`A`	`T`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`AAATTGCTGT`
2L_20746400_20747199_(80	+	75	1.74e-05	`TTTTGATGCA`		`T`	`G`	`C`	`A`	`A`	`T`	`T`	`T`	`T`	`T`	`T`	`T`	`GATTTGCGAC`
X_17508500_17509199_(700	+	647	1.86e-05	`TTTGCCCAAG`		`T`	`G`	`C`	`A`	`G`	`T`	`T`	`T`	`T`	`A`	`T`	`T`	`TAATCAGTGT`
X_11044500_11045199_(700	-	649	2.16e-05	`AGCAGGAGAT`		`T`	`T`	`G`	`T`	`A`	`T`	`T`	`T`	`G`	`T`	`T`	`T`	`TCAACATAAT`
3R_25386700_25387599_(90	+	236	2.16e-05	`ATATTGTTGC`		`T`	`T`	`T`	`T`	`A`	`T`	`T`	`T`	`T`	`A`	`T`	`A`	`TGAACTTAAT`
X_11044500_11045199_(700	-	18	3.34e-05	`TTCCTGTAAA`		`T`	`T`	`G`	`T`	`A`	`A`	`T`	`T`	`T`	`A`	`T`	`T`	`TCAATCTCAT`
X_17508500_17509199_(700	+	491	3.34e-05	`TCAGTTCAAA`		`T`	`T`	`G`	`A`	`A`	`T`	`T`	`T`	`T`	`C`	`A`	`T`	`TGCGAGCGCG`
3R_21504100_21504899_(80	-	232	3.34e-05	`AGGCGGAAAA`		`T`	`T`	`A`	`C`	`T`	`T`	`T`	`T`	`G`	`A`	`T`	`T`	`AATGAAGCGC`
2L_5413600_5414399_(800)	-	147	3.65e-05	`TCGTCCGGTT`		`T`	`T`	`T`	`A`	`T`	`T`	`T`	`A`	`T`	`A`	`T`	`T`	`TCCATGTGCT`

Motif 9 block diagrams

Name

Lowest
p-value

Motifs

2L_5413600_5414399_(800)

3.6e-05

-9

3R_14525400_14526099_(70

6.4e-06

X_17098500_17099199_(700

1.1e-06

-9

X_17508500_17509199_(700

1.9e-05

-9

X_3050400_3051099_(700)

1.9e-06

3R_8837700_8838499_(800)

5e-06

2L_14472300_14473199_(90

5.4e-06

2R_14030000_14030899_(90

6e-06

X_13798600_13799299_(700

1.4e-05

X_9717100_9717899_(800)

7.2e-06

-9

X_16943800_16944599_(800

8.9e-06

3L_6076100_6076799_(700)

9.6e-06

-9

X_10896100_10896799_(700

1.1e-05

3R_25386700_25387599_(90

1.1e-05

-9

2L_11434600_11435499_(90

1.6e-05

2L_20746400_20747199_(80

1.7e-05

X_11044500_11045199_(700

2.2e-05

-9

3R_21504100_21504899_(80

3.3e-05

-9

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

Motif 9 in BLOCKS format

BL   MOTIF 9 width=12 seqs=27
2L_5413600_5414399_(800) (   65) TTAAATTTTATT  1 
3R_14525400_14526099_(70 (  480) TTTAATTTTATT  1 
X_17098500_17099199_(700 (  396) TTGTATTTTATT  1 
X_17508500_17509199_(700 (   16) TTCAATTTTCTT  1 
X_3050400_3051099_(700)  (  623) TTCAATTTGATT  1 
3R_14525400_14526099_(70 (  139) TTCAGTTTTATT  1 
3R_8837700_8838499_(800) (  514) TTATATTTTTTT  1 
X_17508500_17509199_(700 (  249) TTAATTTTTATA  1 
2L_14472300_14473199_(90 (   92) TTAATTTTTATA  1 
2R_14030000_14030899_(90 (    9) TTAAATTTTGTT  1 
3R_14525400_14526099_(70 (  519) TTAGATTTTATT  1 
X_13798600_13799299_(700 (  632) TGCATTTTTATT  1 
X_9717100_9717899_(800)  (  777) TTAATTTTGCTT  1 
X_16943800_16944599_(800 (  783) TTATTTTTTTTT  1 
3L_6076100_6076799_(700) (  173) TTGATTTTGCTT  1 
X_10896100_10896799_(700 (  124) TTGAATTTAATT  1 
3R_25386700_25387599_(90 (   43) GTGAATTTTATT  1 
X_13798600_13799299_(700 (  582) TTTAGTTTTCTT  1 
2L_11434600_11435499_(90 (  122) ATAATTTTTATT  1 
2L_20746400_20747199_(80 (   75) TGCAATTTTTTT  1 
X_17508500_17509199_(700 (  647) TGCAGTTTTATT  1 
X_11044500_11045199_(700 (  649) TTGTATTTGTTT  1 
3R_25386700_25387599_(90 (  236) TTTTATTTTATA  1 
X_11044500_11045199_(700 (   18) TTGTAATTTATT  1 
X_17508500_17509199_(700 (  491) TTGAATTTTCAT  1 
3R_21504100_21504899_(80 (  232) TTACTTTTGATT  1 
2L_5413600_5414399_(800) (  147) TTTATTTATATT  1 
//

Motif 9 position-specific scoring matrix

log-odds matrix: alength= 4 w= 12 n= 22570 bayes= 9.50594 E= 2.7e+005 
  -281  -1140   -269    183 
 -1140  -1140   -111    177 
    51    -11     12    -82 
   143   -269   -269    -23 
   109  -1140   -111     35 
  -281  -1140  -1140    188 
 -1140  -1140  -1140    194 
  -281  -1140  -1140    188 
  -281  -1140    -37    158 
   127    -37   -269    -82 
  -281  -1140  -1140    188 
  -123  -1140  -1140    177

Motif 9 position-specific probability matrix

letter-probability matrix: alength= 4 w= 12 n= 22570 E= 2.7e+005 
 0.037120  0.000089  0.037112  0.925680 
 0.000097  0.000089  0.111159  0.888656 
 0.370330  0.222228  0.259252  0.148190 
 0.703540  0.037112  0.037112  0.222237 
 0.555446  0.000089  0.111159  0.333306 
 0.037120  0.000089  0.000089  0.962703 
 0.000097  0.000089  0.000089  0.999726 
 0.037120  0.000089  0.000089  0.962703 
 0.037120  0.000089  0.185205  0.777586 
 0.629493  0.185205  0.037112  0.148190 
 0.037120  0.000089  0.000089  0.962703 
 0.111167  0.000089  0.000089  0.888656






Time 5043.78 secs.

P N
MOTIF 10 width = 11 sites = 2 llr = 31 E-value = 2.1e+006

NAME	STRAND	START	P-VALUE				SITES
				Simplified	A	:	:	:	:	:	:	:	:	:	:	:
				pos.-specific	C	:	:	:	:	a	:	:	:	:	a	a
				probability	G	a	a	a	a	:	a	:	a	a	:	:
				matrix	T	:	:	:	:	:	:	a	:	:	:	:
.
				bits	2.1
					1.9
					1.7
					1.4
				Information	1.2
				content	1.0
				(22.6 bits)	0.8
					0.6
					0.4
					0.2
					0.0
.
				Multilevel		`G`	`G`	`G`	`G`	`C`	`G`	`T`	`G`	`G`	`C`	`C`
				consensus
				sequence

.

3R_17378100_17378799_(70	-	332	1.60e-07	`TGCATGTTGA`		`G`	`G`	`G`	`G`	`C`	`G`	`T`	`G`	`G`	`C`	`C`	`AGCGATGGGT`
3R_12589500_12590299_(80	+	568	1.60e-07	`CCGTGTGAAG`		`G`	`G`	`G`	`G`	`C`	`G`	`T`	`G`	`G`	`C`	`C`	`TAGAGAGCAG`

Motif 10 block diagrams

Name

Lowest
p-value

Motifs

3R_17378100_17378799_(70

1.6e-07

-10

3R_12589500_12590299_(80

1.6e-07

+10

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 10 in BLOCKS format

BL   MOTIF 10 width=11 seqs=2
3R_17378100_17378799_(70 (  332) GGGGCGTGGCC  1 
3R_12589500_12590299_(80 (  568) GGGGCGTGGCC  1 
//

Motif 10 position-specific scoring matrix

log-odds matrix: alength= 4 w= 11 n= 22600 bayes= 13.4639 E= 2.1e+006 
  -765   -765    206   -765 
  -765   -765    206   -765 
  -765   -765    206   -765 
  -765   -765    206   -765 
  -765    206   -765   -765 
  -765   -765    206   -765 
  -765   -765   -765    193 
  -765   -765    206   -765 
  -765   -765    206   -765 
  -765    206   -765   -765 
  -765    206   -765   -765

Motif 10 position-specific probability matrix

letter-probability matrix: alength= 4 w= 11 n= 22600 E= 2.1e+006 
 0.001298  0.001190  0.996215  0.001298 
 0.001298  0.001190  0.996215  0.001298 
 0.001298  0.001190  0.996215  0.001298 
 0.001298  0.001190  0.996215  0.001298 
 0.001298  0.996215  0.001190  0.001298 
 0.001298  0.001190  0.996215  0.001298 
 0.001298  0.001190  0.001190  0.996323 
 0.001298  0.001190  0.996215  0.001298 
 0.001298  0.001190  0.996215  0.001298 
 0.001298  0.996215  0.001190  0.001298 
 0.001298  0.996215  0.001190  0.001298






Time 5563.94 secs.

P N
SUMMARY OF MOTIFS

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

Name

Combined
p-value

Motifs

3R_12589500_12590299_(80

2.10e-10

-1

-7

-2

-1

+10

-8

3R_25386700_25387599_(90

8.00e-12

-9

-3

-9

-3

-7

-1

-3

3R_21504100_21504899_(80

1.54e-07

-9

-2

-4

-2

2L_5413600_5414399_(800)

1.11e-09

-7

-9

-7

-3

X_14247600_14248299_(700

6.88e-14

-10

-1

-10

-4

3R_17378100_17378799_(70

3.34e-09

-3

-7

-4

-1

-10

-2

2L_14472300_14473199_(90

4.62e-10

-5

-4

3L_1107600_1108399_(800)

2.35e-08

-4

-1

2R_5039100_5039899_(800)

5.67e-07

-2

-5

-3

-1

2L_11434600_11435499_(90

6.40e-10

-3

-1

-3

-1

-3

X_17098500_17099199_(700

2.13e-08

-7

-1

-9

-2

2R_14030000_14030899_(90

2.46e-06

-7

-4

-5

-9

-5

X_17508500_17509199_(700

5.64e-09

-3

-9

-2

-7

-9

-1

-5

-1

-4

X_9717100_9717899_(800)

2.03e-06

-2

-7

-6

-2

-5

-9

X_13798600_13799299_(700

2.86e-12

-4

-3

-4

-7

3R_22366000_22366799_(80

3.71e-04

-9

-2

-6

-7

-2

X_16943800_16944599_(800

1.03e-02

-2

-6

X_11044500_11045199_(700

3.17e-06

-9

-5

-4

-9

2R_6957200_6957899_(700)

4.37e-11

-10

-4

-2

-1

-3

-1

-3

-4

2R_14356700_14357399_(70

5.82e-12

+10

-1

-2

2L_20746400_20747199_(80

7.92e-11

-4

-8

-1

3R_8837700_8838499_(800)

6.37e-12

-7

-3

-5

-7

-4

X_17980400_17981199_(800

2.95e-09

-6

-5

-1

-3

-7

-1

X_10896100_10896799_(700

2.09e-05

-2

-6

-8

X_8717700_8718299_(600)

1.13e-09

-1

-4

-7

-6

-1

3L_19484500_19485299_(80

6.33e-02

-2

-5

-2

2R_8758700_8759399_(700)

6.77e-09

-6

-4

-8

-4

3L_6076100_6076799_(700)

2.97e-08

-9

-1

-3

X_3050400_3051099_(700)

5.15e-07

-8

-5

-8

-1

-4

3R_14525400_14526099_(70

2.75e-09

-4

-3

-1

-4

-9

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

Stopped because nmotifs = 10 reached.


CPU: padouk

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 = 12 sites = 50 llr = 668 E-value = 8.0e-093

P N MOTIF 2 width = 12 sites = 50 llr = 538 E-value = 4.5e-036

P N MOTIF 3 width = 12 sites = 35 llr = 406 E-value = 1.2e-026

P N MOTIF 4 width = 12 sites = 34 llr = 360 E-value = 3.4e-010

P N MOTIF 5 width = 11 sites = 23 llr = 258 E-value = 6.8e-006

P N MOTIF 6 width = 11 sites = 26 llr = 274 E-value = 4.9e-002

P N MOTIF 7 width = 11 sites = 30 llr = 314 E-value = 4.7e-006

P N MOTIF 8 width = 8 sites = 16 llr = 176 E-value = 3.1e-001

P N MOTIF 9 width = 12 sites = 27 llr = 270 E-value = 2.7e+005

P N MOTIF 10 width = 11 sites = 2 llr = 31 E-value = 2.1e+006

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 = 12 sites = 50 llr = 668 E-value = 8.0e-093

P N
MOTIF 2 width = 12 sites = 50 llr = 538 E-value = 4.5e-036

P N
MOTIF 3 width = 12 sites = 35 llr = 406 E-value = 1.2e-026

P N
MOTIF 4 width = 12 sites = 34 llr = 360 E-value = 3.4e-010

P N
MOTIF 5 width = 11 sites = 23 llr = 258 E-value = 6.8e-006

P N
MOTIF 6 width = 11 sites = 26 llr = 274 E-value = 4.9e-002

P N
MOTIF 7 width = 11 sites = 30 llr = 314 E-value = 4.7e-006

P N
MOTIF 8 width = 8 sites = 16 llr = 176 E-value = 3.1e-001

P N
MOTIF 9 width = 12 sites = 27 llr = 270 E-value = 2.7e+005

P N
MOTIF 10 width = 11 sites = 2 llr = 31 E-value = 2.1e+006

P N
SUMMARY OF MOTIFS