Hi Ke,
Sorry I have been slow to follow up. Just wanted to bring to your attention the pre-release announcement from today - https://groups.google.com/forum/#!topic/sequenceserver/vuuRHmqg6YA which adds graphical output and makes available correct hit and hsp coordinates on the server and in the browser. You can also download XML and tabular report for downstream analysis.
Additionally, we use the powerful biojs-vis-sequence widget in the browser to visualise hit sequences. biojs-vis-sequence can be used to highlight / annotate hsps on the hit sequence. We didn’t get the chance to make that happen. But if you would like to take a shot, here’s the biojs-vis-sequence API documentation and an experimental commit from me exploring annotation functionality:
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http://www.ebi.ac.uk/Tools/biojs/registry/Biojs.Sequence.html
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https://github.com/yeban/sequenceserver/commit/fb2712e35e5b346240ad96f7e6e985f371034447
– Priyam