Apoptotic ladder is a result of activation of a Caspase Activated DNAse, and as it cuts between the nucleosomes, so the size of the resulting fragments is the lenght of the DNA around nucleosome and multiples of it. The fragments are therefore about 180 bp long and multiples of it (180 bp, 360 bp, 540 bp and so on).

We usually visualize apoptotic ladder using 1.8% agarose gel, so a lot more concentrated than used by You and thus the smaller fragments are more sharp and have better visibility (it could be one of Your problems). One of our results I am attaching as the photo.

Thanks a lot Patrycja and Omer....shall try this one soon and keep you updated :)