During gel electrophoresis, I found the illumination within wells only. And in some cases, a band is also seen along with the illumination within well. What is the reason?
Could be that your gel is too dense for your sample, or that the sample size is too large for the agarose concentration used. does this happen for the ladder as well, or is it sample only? if sample is too big for the gel, it will stay in the pocket, thereby illumination the pocket.
There could be many reasons. Some of which are given below.
1) The DNA may not have been extracted properly or the gel preparation may be poor. The comb may not have been placed correctly or the gel must have been disturbed during the removal of the comb. Because of these reasons, the DNA is unable to come out from the well.
The wells may have been broken during sample loading or the air bubbles may have been formed during gel casting. These air bubbles inside the wells could hinder DNA from migrating towards the positive pole.
2) Re-using the gel may limit the migration of DNA.
3) The concentration of DNA may be very high in the well.
4) The DNA may be highly contaminated with proteins.
Well, your DNA ladder looks great. To me, the bands up by the well look like gDNA. There are other molecules that will light up in a gel and show up (secondary metabolites etc.)
What size is the band you are hoping to see?
If your bands are faint it can help to remove the gel from the running tray as those do absorb some of the UV light.