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#!/usr/bin/perl
open(FILE,"align.input") or die "can not open file: $!";
...
        ($str1,$str2)=();
    }
}

        my @mismatch;
        for($i=0;$i<=length($str1);$i++)
...
        if(@mismatch) {
            print "mismatch: @mismatch\n";
        }

>hit    tstart    tend    #query    qstart    matches    qend    score
+    probability    mismatches
>gi|122939163|ref|NM_000165.3|    1595    1630    SNPSTER4_104_308EFAA
+XX:1:1:1694:128    1    35    36    -10    1.000000    1
mismatch: 30.GA
>gi|113412254|ref|XR_018775.1|    1578    1613    SNPSTER4_104_308EFAA
+XX:1:1:1608:94    1    36    36    0    0.090884    0
mismatch: 3.GT 34.TG

        my $xor = $str1 ^ $str2;
        while($xor =~ /[^\0]/g) {
            my $i = pos($xor) - 1;  # or: $-[0]
            push @mismatch, "$i." . substr($str1,$i,1) . substr($str2,
+$i,1);
        }