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sxoght: #query  hit     score   probability     qstart  qend    qorien
+tation    tstart  tend    matches mismatches      gapOpening      gap
+s
@SNPSTER4_104_308EFAAXX:1:1:1694:128
...
Query:          1 GCAGTTTTAAGTTATTAGTTTTTAAAATCAGTACTT 36
                  ||| |||||||||||||||||||||||||||||| |
Sbjct:       1578 GCATTTTTAAGTTATTAGTTTTTAAAATCAGTACGT 1613

>gi|122939163|ref|NM_000165.3|    1595    1630    SNPSTER4_104_308EFAA
+XX:1:1:1694:128    1    36    36    -10    1    1.000000    35    
mismatch : 1625.GA        
>gi|113412254|ref|XR_018775.1|    1578    1613    SNPSTER4_104_308EFAA
+XX:1:1:1608:94    1    36    36    0    1    0.090884    36    
mismatch : 1581.GT 1612.TG

#!/usr/bin/perl
open(FILE,"align.input") or die "can not open file";
...
    }
    }
}