Hi Ubaid,

having such differences from both strands of your sequence only means that your sequence primers are not fully well designed. I guess you did sanger sequencing and that the electrophoregram shows you a noisy sequence at forward? unless you'll have designed new primers with the results you have, you canut conclude, even if I would at your place.

fred

Hi Fred,

Yes I did Sanger sequencing and I have used universal primers for my analysis. But still it's showing this much difference between forward and reverse sequences. Shall I move forward with these results or I need to do something else as I have used universal primers.

it really depends on the positioning of the poorly fitting bases. Bases near the primer in sanger sequencing are poorly sequenced and should be trimmed off prior to analysis.Similarly bases at the other end..above 900 bases for instance may be quite weak and confused with the background so give poor sequence and should be trimmed.

If all of your poorly matching bases are at one end of the sequence it could be that hairpin formation is spoiling the sequence in a high GC region and the amplimer simply sequences better in one direction than the other. In answer to your question if the signal to noise ratio is good for part of the sequence then you should trust that part of the sequence and blast it. If you post the ,abi sequence files it would provide useful information as to which parts of the sequence are of good quality

HI Ubaid

Paul gave you really good advices, as he always do, but I would add that if your universal primers are not enough good to obtain what you're searching for, using the sequence you had could help you in designing new primers.

fred