==============================================================
                     PRIMA v1.0 (Windows)

     Copyright C. Linhart, R. Elkon, R. Sharan, R. Shamir
                  Tel-Aviv University, 2003.
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 TF PWMs file ...................... matrix_E2F.dat
 BG promoters file ................. bg.all.13K.llid
 Target sets promoters file ........ tar.hcc.568.llid
 Complement strand Flag ............ 1
 False-positives rate .............. 1 per 10 promoters
 Min. number of BG's to cover ...... 0
 Input threshold ................... [None]


Target set #0 : 568 promoters.
Read 1 target set.
Read 12981 BG promoters.
Finished reading BG and target sets data, and promoters files.
Promoters are of length 1201.
Average effective length (number of non-masked windows of length 10 in a promoter) is 893.

BG promoters 3-tuples frequencies: 
 ij   \    k     A (0.241)   C (0.257)   G (0.258)   T (0.244)  
 AA (0.071)     0.025       0.012       0.018       0.015    
 AC (0.048)     0.015       0.013       0.006       0.013    
 AG (0.073)     0.019       0.018       0.022       0.014    
 AT (0.050)     0.011       0.010       0.013       0.016    
 CA (0.066)     0.015       0.015       0.023       0.013    
 CC (0.081)     0.020       0.026       0.013       0.022    
 CG (0.037)     0.006       0.013       0.013       0.006    
 CT (0.072)     0.010       0.021       0.023       0.019    
 GA (0.061)     0.018       0.012       0.021       0.010    
 GC (0.067)     0.016       0.021       0.013       0.017    
 GG (0.081)     0.020       0.021       0.026       0.013    
 GT (0.049)     0.008       0.012       0.016       0.013    
 TA (0.043)     0.014       0.008       0.010       0.011    
 TC (0.061)     0.015       0.020       0.006       0.019    
 TG (0.067)     0.016       0.016       0.020       0.016    
 TT (0.073)     0.014       0.018       0.015       0.026    


==> Generating 1000 random sequences of length 907 according to BG frequencies.

==> Finding binding-sites of TF PWMs in sequences.

--> PWM #1: M00000 [E2F_12] (length 12): 

 Random promoters:
   Hit threshold set to 2162.2.
   Found total of 103 hits out of 1792000 possible windows.
   100 out of 1000 promoters contain one or more hits.

 BG set:
   Hit threshold set to 2162.2.
   Found total of 649 hits out of 23077950 possible windows.
   615 out of 12981 promoters contain one or more hits.
   Number of promoters with 0,1,2,3+ hits is 12366,583,30,2, respectively.

 Target set #0:
   Found total of 68 hits out of 999658 possible windows.
   62 out of 568 promoters contain one or more hits.
   Hyper-geometric enrichment score p-value: 2.6e-010


--> PWM #2: M99999 [DUMMY] (length 11): 

 Random promoters:
   Hit threshold set to 570.2.
   Found total of 101 hits out of 1794000 possible windows.
   96 out of 1000 promoters contain one or more hits.

 BG set:
   Hit threshold set to 570.2.
   Found total of 1775 hits out of 23134468 possible windows.
   1573 out of 12981 promoters contain one or more hits.
   Number of promoters with 0,1,2,3+ hits is 11408,1397,151,25, respectively.

 Target set #0:
   Found total of 74 hits out of 1002152 possible windows.
   65 out of 568 promoters contain one or more hits.
   Hyper-geometric enrichment score p-value: 6.7e-001


Done.

PRIMA citation:
  Elkon, R., Linhart, C., Sharan, R., Shamir, R., and Shiloh, Y.,
  "Genome-wide In-silico Identification of Transcriptional Regulators
   Controlling Cell Cycle in Human Cells", Genome Research, Vol. 13(5), pp. 773-780, 2003.