[Biojava-l] Blast XML output question

[tai kwan do]

Hello,

I'm seeing a difference in the data being output by stand-alone blast and 
online blast.  The identities value are different between the xml output and 
the text output.  The other difference I see is in the query and hit 
sequences.  I've included below the outputs using the same input parameters, 
does anyone know why this is the case?

    gb|AE000111.1|AE000111 Escherichia coli K-12 MG1655 section 1 of 400 of 
the complete

          genome
         Length = 10596

Score =  589 bits (297), Expect = e-168
Identities = 315/324 (97%)
Strand = Plus / Plus


Query: 237 aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtg 296
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237 aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtg 296


Query: 297 cgggcnnnnnnnnncgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcgg 356
          |||||         ||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 297 cgggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcgg 356


Query: 357 cggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaa 416
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 357 cggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaa 416


Query: 417 tgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacct 476
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 417 tgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacct 476


Query: 477 ggtggcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgc 536
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 477 ggtggcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgc 536


Query: 537 cgaacgtatttttgccgaactttt 560
          ||||||||||||||||||||||||
Sbjct: 537 cgaacgtatttttgccgaactttt 560


       <Hit>
         <Hit_num>1</Hit_num>
         <Hit_id>gi|1786181|gb|AE000111.1|AE000111</Hit_id>
         <Hit_def>Escherichia coli K-12 MG1655 section 1 of 400 of the 
complete genome</Hit_def>
         <Hit_accession>AE000111</Hit_accession>
         <Hit_len>10596</Hit_len>
         <Hit_hsps>
           <Hsp>
             <Hsp_num>1</Hsp_num>
             <Hsp_bit-score>589.253</Hsp_bit-score>
             <Hsp_score>297</Hsp_score>
             <Hsp_evalue>1.04898e-168</Hsp_evalue>
             <Hsp_query-from>237</Hsp_query-from>
             <Hsp_query-to>560</Hsp_query-to>
             <Hsp_hit-from>237</Hsp_hit-from>
             <Hsp_hit-to>560</Hsp_hit-to>
             <Hsp_query-frame>1</Hsp_query-frame>
             <Hsp_hit-frame>1</Hsp_hit-frame>
             <Hsp_identity>324</Hsp_identity>
             <Hsp_positive>324</Hsp_positive>
             <Hsp_align-len>324</Hsp_align-len>
             
<Hsp_qseq>AGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT</Hsp_qseq>
             
<Hsp_hseq>AGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT</Hsp_hseq>
             
<Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
           </Hsp>
           <Hsp>

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