[Bioperl-l] something wrong with my code?

[Ambrose Ng]

my code here:
		
my @s_ind = $hsp->seq_inds('hit', 'id', 1);
print "conserved=", my $s_ind = join (" ", at s_ind), "\n";

reports this:

conserved=7896-8225 8249-8949


but the numbers are different from the blast report.

Is it more likely to do with my code or is there something going on with the 
bioperl module compatibility with this blast report that I'm 
misunderstanding?

Ambrose

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Query=  gnl|UG|Os#S16394561 Oryza sativa (japonica cultivar-group) cDNA clone:00
2-141-A12, full insert sequence /gb=AK108259 /gi=32993468 /ug=Os.4 /len=1031
        (1031 letters)

Database:  /fdf/coe05/gm0/0/rice_Chr1f.dna
           426 sequences; 63,195,892 total letters.
Searching.......................................................done.

                                                               Score     E
Sequences producing significant alignments:                    (bits)  Value

o_sativa|chr_1|OJ1116_H09|6985                                  1933  0.0

>o_sativa|chr_1|OJ1116_H09|6985
            Length = 110086

 Score = 1933 bits (975), Expect = 0.0
 Identities = 1031/1124 (91%)
 Strand = Plus / Plus


Query: 1    aagctagctcgcgcgcaaattaatcgccgatcgatcctacgatgaagcggaagcggccgg 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7826 aagctagctcgcgcgcaaattaatcgccgatcgatcctacgatgaagcggaagcggccgg 7885


Query: 61   cggcgctgcgcggcggggaggaggcggcggcggcggcgctgaagcgtgggccgtggacgc 120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7886 cggcgctgcgcggcggggaggaggcggcggcggcggcgctgaagcgtgggccgtggacgc 7945


Query: 121  ccgaggaggacgaggtgctggcgcggttcgtggcgcgggaggggtgcgaccggtggcgca 180
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7946 ccgaggaggacgaggtgctggcgcggttcgtggcgcgggaggggtgcgaccggtggcgca 8005


Query: 181  cgctgccgcggcgcgcgggcctgctgcgctgcggcaagagctgccgcctccggtggatga 240
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8006 cgctgccgcggcgcgcgggcctgctgcgctgcggcaagagctgccgcctccggtggatga 8065


Query: 241  actacctccgccccgacatcaagcgctgccccatcgccgacgacgaggaggacctcatcc 300
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8066 actacctccgccccgacatcaagcgctgccccatcgccgacgacgaggaggacctcatcc 8125


Query: 301  tccgcctccaccgcctcctcggcaaccggt---------------------------ggt 333
            ||||||||||||||||||||||||||||||                           |||
Sbjct: 8126 tccgcctccaccgcctcctcggcaaccggtaagca<--[8161:8243]-->taggtggt 8251


Query: 334  cgctgatcgccgggaggttgccggggcgcacggacaacgagatcaagaactactggaact 393
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8252 cgctgatcgccgggaggttgccggggcgcacggacaacgagatcaagaactactggaact 8311


Query: 394  cgcatctcagcaagaagctcatcgcgcagggcatcgacccgcggacgcacaagccgctga 453
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8312 cgcatctcagcaagaagctcatcgcgcagggcatcgacccgcggacgcacaagccgctga 8371


Query: 454  cggccgccgccgatcactccaacgccgccgctgccgtcgccgccacttcttacaagaagg 513
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8372 cggccgccgccgatcactccaacgccgccgctgccgtcgccgccacttcttacaagaagg 8431


Query: 514  cggtgccggccaagccgccgaggacggcatcctcgccggccgctggcattgagtgcagcg 573
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8432 cggtgccggccaagccgccgaggacggcatcctcgccggccgctggcattgagtgcagcg 8491


Query: 574  acgatcgtgcccgaccggccgacggtggcggtgacttcgcagcgatggtgagcgccgccg 633
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8492 acgatcgtgcccgaccggccgacggtggcggtgacttcgcagcgatggtgagcgccgccg 8551


Query: 634  atgccgagggattcgaaggaggatttggcgatcagttctgtgccgaggatgcagttcatg 693
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8552 atgccgagggattcgaaggaggatttggcgatcagttctgtgccgaggatgcagttcatg 8611


Query: 694  gtggcttcgacatgggttccgcttccgccatggtgggtgacgacgacttctcctcgtttc 753
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8612 gtggcttcgacatgggttccgcttccgccatggtgggtgacgacgacttctcctcgtttc 8671


Query: 754  ttgattctctgatcaacgacgagcagttaggcgatctcttcgtcgtcgagggcaacgatc 813
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8672 ttgattctctgatcaacgacgagcagttaggcgatctcttcgtcgtcgagggcaacgatc 8731


Query: 814  acgagcatggcaatggtgagattggtcatggagacgtcatggaatccaaacagtaatctt 873
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8732 acgagcatggcaatggtgagattggtcatggagacgtcatggaatccaaacagtaatctt 8791


Query: 874  tcgggagattgatcagggaataagttgaccatgagaaaacatgtaagaacagcttgtctg 933
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8792 tcgggagattgatcagggaataagttgaccatgagaaaacatgtaagaacagcttgtctg 8851


Query: 934  ctgagtcatgaccggtgatgtgtatgtgatggaagaaaacgtatgtacgacttaatgctt 993
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8852 ctgagtcatgaccggtgatgtgtatgtgatggaagaaaacgtatgtacgacttaatgctt 8911


Query: 994  gcacctatactactgctgtgtgcattattcgagtgatc 1031
            ||||||||||||||||||||||||||||||||||||||
Sbjct: 8912 gcacctatactactgctgtgtgcattattcgagtgatc 8949