#!/usr/bin/perl
open(FILE,"align.input") or die "can not open file: $!";
while($var=<FILE>){
    if($var=~/^sxoght:/){
        ($str1,$str2)=();
        @ar=split(/\s+/,$var);
        print ">$ar[2]\t$ar[8]\t$ar[9]\t$ar[1]\t$ar[5]\t$ar[10]\t$ar[6]\t$ar[3]\t$ar[4]\t$ar[11]\n";
    }
    if($var=~/^Query:/){
        $str1=$var;
        $str1=~s/^Query:\s+//g;
        $str1=~s/\d+\s+//g;
        $str1=~s/\s+//g;
    }
    if($var=~/^Sbjct:/){
        $str2=$var;
        $str2=~s/^Sbjct:\s+//g;
        $str2=~s/\d+\s+//g;
        $str2=~s/\s+//g;
    }
    if(defined $str1 and defined $str2) {
        for($i=0;$i<=length($str1);$i++)
        {
            if(substr($str1,$i,1) ne substr($str2,$i,1)){
                # this is not in the desired format, yet
                print substr($str1,$i,1);
                print substr($str2,$i,1);
                print "$i\n";
            }
        }
        ($str1,$str2)=();
    }
}

##</code><code>##

        my @mismatch;
        for($i=0;$i<=length($str1);$i++)
        {
            if(substr($str1,$i,1) ne substr($str2,$i,1)){
                push @mismatch, "$i." . substr($str1,$i,1) . substr($str2,$i,1);
            }
        }
        if(@mismatch) {
            print "mismatch: @mismatch\n";
        }

##</code><code>##

>hit	tstart	tend	#query	qstart	matches	qend	score	probability	mismatches
>gi|122939163|ref|NM_000165.3|	1595	1630	SNPSTER4_104_308EFAAXX:1:1:1694:128	1	35	36	-10	1.000000	1
mismatch: 30.GA
>gi|113412254|ref|XR_018775.1|	1578	1613	SNPSTER4_104_308EFAAXX:1:1:1608:94	1	36	36	0	0.090884	0
mismatch: 3.GT 34.TG

##</code><code>##

        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);
        }