meme.farntrans5.oops

EM算法的改进

Multilevel           CQDEETGGFSDKPGADVDFYHT
consensus            TCECKAP LAKRDEDEA LF S
sequence               KKLK  IL N  EHR P   
                       QTPQ   R    KMS V   
                                   NS      
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                     Site       
-------------             ----- ---------            ----------------------
RATRABGERB                  270  6.22e-24 REKLRSFILA CQDEETGGFADRPGDMVDPFHT LFGIAGLSLL
BET2_YEAST                  266  9.66e-22 YEKLTEFILK CQDEKKGGISDRPENEVDVFHT VFGVAGLSLM
RAM1_YEAST                  343  3.50e-21 HALRDYILYC CQEKEQPGLRDKPGAHSDFYHT NYCLLGLAVA
PFTB_RAT                    342  3.58e-19 QQALQEYILM CCQCPAGGLLDKPGKSRDFYHT CYCLSGLSIA
CAL1_YEAST                  321  4.79e-14 ELVTNYLLDR TQKTLTGGFSKNDEEDADLYHS CLGSAALALI
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
RATRABGERB                        6.2e-24  269_[2]_40
BET2_YEAST                        9.7e-22  265_[2]_38
RAM1_YEAST                        3.5e-21  342_[2]_67
PFTB_RAT                          3.6e-19  341_[2]_74
CAL1_YEAST                        4.8e-14  320_[2]_34
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=22 seqs=5
RATRABGERB               (  270) CQDEETGGFADRPGDMVDPFHT  1 
BET2_YEAST               (  266) CQDEKKGGISDRPENEVDVFHT  1 
RAM1_YEAST               (  343) CQEKEQPGLRDKPGAHSDFYHT  1 
PFTB_RAT                 (  342) CCQCPAGGLLDKPGKSRDFYHT  1 
CAL1_YEAST               (  321) TQKTLTGGFSKNDEEDADLYHS  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 22 n= 1795 bayes= 8.48382 E= 4.4e-013 
  -317    468   -536   -480   -473   -515   -489   -393   -501   -496   -358   -431   -496   -481   -434   -439   -203   -421   -573   -551 
  -201    -29   -352   -110   -388   -392    -45   -322   -218   -293   -129   -177   -279    435   -152   -273   -235   -302   -327   -387 
  -101   -461    226    200   -366   -252   -171   -296    142   -325   -195    -63   -210    179   -106   -160   -127   -232   -399   -310 
   -39    127    -87    196   -231   -185    -80   -180    159   -219    -88      2   -154     14      7    -69    148   -136   -274   -193 
   -54   -354    -66    215   -262   -208   -104   -209    154     -4   -113    -26    160      9    -17    -97    -59   -161   -303   -220 
   109   -318   -107    -17   -246   -198    -89   -192    159   -232    -97    -10   -164    171     12    -63    240   -146   -282   -206 
  -155   -406   -271   -314   -437    348   -337   -418   -283   -497   -338   -171     32   -334   -265   -240   -290   -356   -399   -415 
  -175   -426   -285   -331   -447    358   -350   -432   -297   -511   -353   -187   -359   -350   -276   -260   -314   -374   -405   -425 
  -253   -339   -527   -442    287   -470   -372    161   -402    180     35   -379   -390   -333   -355   -390   -242    -73   -270   -215 
   145   -249   -160    -78   -208   -199   -131   -136    -22     -8    -77    -49   -178    -48    140    187     10    -99   -272   -203 
  -261   -452    373    -63   -408   -335   -255   -377    -56   -443   -329    -19   -380   -253   -275   -283   -285   -345   -421   -376 
  -190   -410   -273   -160   -400   -304   -149   -302    299   -321   -201    170   -285    -45    295   -221   -166   -272   -344   -309 
  -106   -385     26   -217   -346   -298   -272   -305   -205   -329   -260   -202    420   -198   -216   -191   -175   -256   -429   -395 
  -146   -418   -139    169   -425    311   -268   -389   -185   -445   -306    -99   -299   -178   -218   -207   -226   -324   -414   -385 
   110   -357    131    152   -267   -184    -93   -229    149   -257   -123    190   -164      6    -33    -82    -53   -176   -307   -218 
   -36   -329    116    133   -229   -179    182   -199     27   -229    211     15   -149     22    -11     73    -33   -150   -276   -173 
   155   -224   -224   -142   -204   -219   -182    -48    -94   -184    -75   -118   -213   -114    115     44    -57    264   -288   -237 
  -290   -459    383    -92   -417   -370   -283   -389   -348   -461   -350    -36   -415   -318   -335   -325   -328   -361   -427   -393 
  -143   -250   -386   -311    340   -342   -256    -34   -272     39    -12   -246     91   -255   -252   -242   -142     97   -205    -69 
  -229   -329   -362   -321    283   -383    -55   -236   -290   -245   -169   -229   -322   -266   -247   -273   -258   -228    -63    367 
  -338   -410   -309   -336   -261   -388    482   -419   -349   -382   -264    -93   -347    -94   -179   -298   -276   -368   -304   -128 
  -145   -275   -320   -331   -332   -339   -304   -212   -239   -361   -157   -102   -300   -226   -230     94    393   -169   -371   -379 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 22 nsites= 5 E= 4.4e-013 
 0.000000  0.800000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000 
 0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.800000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.400000  0.200000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.200000  0.000000  0.400000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.400000  0.000000  0.000000  0.000000  0.000000  0.200000  0.200000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.400000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.800000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.400000  0.000000  0.000000  0.200000  0.000000  0.400000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.200000  0.400000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.800000  0.000000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.400000  0.000000  0.000000  0.200000  0.000000  0.000000  0.400000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.800000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.400000  0.000000  0.600000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.200000  0.000000  0.200000  0.200000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.200000  0.200000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000 
 0.200000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.200000  0.200000  0.000000  0.400000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.400000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.400000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.600000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.200000  0.800000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[CT][QC][DEKQ][ECKT][EKLP][TAKQ][GP]G[FLI][SALR][DK][KRN][PD][GE][ADEKN][DEHMS][VARS]D[FLPV][YF]H[TS]
--------------------------------------------------------------------------------




Time  1.17 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
RAM1_YEAST                       2.79e-40  291_[1(5.02e-27)]_19_[2(3.50e-21)]_67
PFTB_RAT                         1.99e-40  133_[1(5.98e-09)]_19_[1(4.93e-05)]_16_[1(4.59e-09)]_17_[1(3.39e-29)]_28_[2(3.58e-19)]_74
BET2_YEAST                       6.69e-48  66_[2(1.66e-05)]_31_[1(4.59e-09)]_16_[1(7.38e-08)]_19_[1(6.77e-34)]_15_[2(9.66e-22)]_38
RATRABGERB                       9.89e-49  126_[1(2.24e-09)]_16_[1(4.67e-06)]_16_[1(1.47e-32)]_15_[2(6.22e-24)]_40
CAL1_YEAST                       2.37e-33  270_[1(5.02e-27)]_18_[2(4.79e-14)]_34
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 2 reached.
********************************************************************************

CPU: chromo.imb.uq.edu.au

********************************************************************************