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Old 01-31-2012, 06:24 AM   #1
jomaco
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Location: Sheffield

Join Date: Oct 2011
Posts: 26
Default Standalone Blast output

Hi

When looking at the output from standalone blast I see this:

<Hsp_hit-from>76056</Hsp_hit-from>
<Hsp_hit-to>76901</Hsp_hit-to>
<Hsp_query-frame>0</Hsp_query-frame>
<Hsp_hit-frame>3</Hsp_hit-frame>
<Hsp_identity>89</Hsp_identity>
<Hsp_positive>141</Hsp_positive>
<Hsp_gaps>19</Hsp_gaps>
<Hsp_align-len>286</Hsp_align-len>

Can anyone tell me why is the align length less than "hit-to" minus "hit-from"?

Is there a description of the output available anywhere, maybe I am looking at this wrongly. Hope you can help

Thanks
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