[RNase]

Is there a difference in efficiency of ligation between 5'-overhang and 3'-overhang? And do ligation products look like dsDNA? I don't understand how there are several ligation products when the PCR fragment digested by a restriction enzyme has the same sequence.

[Babcock_Hall]

I am not following you.  Do you mean that there is a PCR fragment that was digested by one restriction endonuclease, as opposed to two endonucleases?  Is it being mixed with a different fragment before the ligation?