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The blast hit document returned is a summary document and does not contain the full GenBank record for that sequence. This alignment view only shows the region of alignment between the query and the hit sequence. Like any other alignment in Geneious, you can zoom into display the bases, change the color settings, and highlight agreements or disagreements to the consensus in the General controls to the right of the viewer. You can see from the green identity graph above the alignment that the two sequences are identical. Click on the hit to NP_001014408 and you should see something like this:
![geneious convert sequencher spf file geneious convert sequencher spf file](https://www.snapgene.com/wordpress/wp-content/uploads/2016/09/GenBank.jpg)
Now that you have a set of search results, you should look at some alignments. Geneious also produces a Grade score, which combines query coverage, e-value and identity values for each hit with weights 0.5, 0.25 and 0.25 respectively, allowing you to determine the longest, highest identity hits. This is why alignments tend to be ranked by their E Value rather than identity. The identity refers only to the aligned region so it is possible to have very short alignments which have high identity. This is because the alignment produced is a local similarity alignment and it has aligned the maximum region it could find between the two sequences. You can see that many of the hits in this example are 100% identical to the query over the length of the alignment, but have different Sequence Lengths. This is also useful as it will indicate how similar the sequence found in the database is to the one you used as a query. In addition to the E Value, there is also a column labelled % Pairwise Identity. You should take these statistics as a guide as there can still be interesting alignments that appear far less significant. You may even have examples where the E Value reads 0.00e+00 and this is telling you that statistically there is no likelihood that this alignment has happened by chance.
![geneious convert sequencher spf file geneious convert sequencher spf file](https://s.getwinpcsoft.com/screenshots/4234/4234469_3.jpg)
This is a very small number and indicates that it is highly unlikely that this alignment would ever occur by chance. The top hit shown here as 1.18e-107 is the same as 1.18×10 -107. For E values, the smaller the number the better.
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