sxoght: #query  hit     score   probability     qstart  qend    qorientation    tstart  tend    matches mismatches      gapOpening      gaps
@SNPSTER4_104_308EFAAXX:1:1:1694:128
GGGATAAGAGAGGTGCATGTTGGTATTTAAGGTAGT
1 alignment(s) -- reports limited to 10 alignment(s)

sxoght: SNPSTER4_104_308EFAAXX:1:1:1694:128     gi|122939163|ref|NM_000165.3|   -10     1.000000        1       36      +       1595    1630    35      1   00
Score = -10, P(A|R) = 1.000000
Query:          1 GGGATAAGAGAGGTGCATGTTGGTATTTAAGGTAGT 36
                  |||||||||||||||||||||||||||||| |||||
Sbjct:       1595 GGGATAAGAGAGGTGCATGTTGGTATTTAAAGTAGT 1630

@SNPSTER4_104_308EFAAXX:1:1:1608:94
GCAGTTTTAAGTTATTAGTTTTTAAAATCAGTACTT
14 alignment(s) -- reports limited to 10 alignment(s)

sxoght: SNPSTER4_104_308EFAAXX:1:1:1608:94      gi|113412254|ref|XR_018775.1|   0       0.090884        1       36      +       1578    1613    36      0   00
Score = 0, P(A|R) = 0.090884
Query:          1 GCAGTTTTAAGTTATTAGTTTTTAAAATCAGTACTT 36
                  ||| |||||||||||||||||||||||||||||| |
Sbjct:       1578 GCATTTTTAAGTTATTAGTTTTTAAAATCAGTACGT 1613

##</code><code>##

>gi|122939163|ref|NM_000165.3|	1595	1630	SNPSTER4_104_308EFAAXX: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_308EFAAXX:1:1:1608:94	1	36	36	0	1	0.090884	36	
mismatch : 1581.GT 1612.TG	

##</code><code>##

#!/usr/bin/perl
open(FILE,"align.input") or die "can not open file";
while($var=<FILE>){
	$str1=();$str2=();
	if($var=~/^sxoght:/){
		@ar=split(/\s+/,$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;
		$str2=~s/\s+//g;
	}
	for($i=0;$i<=length($str1);$i++)
	{
	if(substr($str1,$i,1) ne substr($str2,$i,1)){
		print substr($str1,$i,1);
		print substr($str2,$i,1);
		print "$i\n";		
	}
	}
}