Sma I degrading ends

[Anthony Tomlinson]

In article <940811144046.201d52 at thorin.uthscsa.edu> ,
HARDIES at THORIN.UTHSCSA.EDU writes:
>I am guessing that you detected the lost bases after transforming and 
>recovering a clone.  In that case, your problem may be at the ligation
>step.  If ligation fails, then you transform with the linear fragment
>and E. coli circularizes it by invading with one end at a target
>internal to the other (at low efficiency).  The result fits your 
>description.  
>

Is there any preference by the coli apparatus for certain sequences? How
does it know where the end is, and yet still invade a variable distance
from the end?  Sorry to ask dumn questions, but I've never heard of this
before, and it could explain a problem or two if mine.....

Thanks
Anthony