There are a number of factors that would help determine what is considered good sequence data. First, how did you go about determining the sequence for the gene? If this was done by basic Sanger sequencing, do you have multiple results to cover the length of the gene? Typically we would sequence genes that require more than a single result. 

I would also look at the electropherogram and note the quality of the peaks. As Roopesh suggested, ABI software provides a quality score for each peak. This could help determine where resolution and quality begins to fall off. If you are trying to compare sequence bases in the later part of the sequence, this could lower the percent homology with the gene. You may need to continue downstream by selecting another primer from you sequence result assuming this is from Sanger sequencing.

Is the gene you are using for comparison highly conserved? In other words, would you expect that the experimental sequence may have 100 percent homology with the gene? 

These would be some of the factors to consider when determining what homology a sequence result should provide.

Thanks

Quality of the sequencing is very important. Did you make the sequencing in both directions??

You received a quality sequencing file with your sequence. it s important to have a look on the peaks.

Dear/ Nermeen your percent of sequencing revealed to circulation of  a new strain with replacement of nucleic acid and amino acids protein. Please look at my published paper  online:.

American Journal of Epidemiology and Infectious Disease, 2014, Vol. 2, No. 3, 74-82

Available online at http://pubs.sciepub.com/ajeid/2/3/2

© Science and Education Publishing

DOI:10.12691/ajeid-2-3-2