I'm not sure if I've quite understood your question, but just in case I have:

#!/usr/bin/perl -w
use strict;

chomp(my @list = grep /^(?:Query|Sbjct) /, <>);
s/^\w*\s+\d*\s+([^\s]+).*/$1/ for @list;

for my $i (0 .. @list / 2 - 1){
    my $mm;
    my @a = split //, $list[$i*2];
    my @b = ('|') x @a;
    my @c = split //, $list[$i*2+1];

    for (0..$#a){
        if (uc($a[$_]) ne uc($c[$_])){
            $b[$_] = ' ';
            $mm .= "Mismatch ($a[$_]/$c[$_]) at position " . ($_ + 1) 
+. "\n";
        }
    }
    print @a, "\n", @b, "\n", @c, "\n";
    print $mm ? "$mm\n" : "\n";
}
[download]

Running the above script with your (tweaked to produce errors) file as an argument, the output is

TGtAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCATCGCCTCCTGGGTTCACGCCATT
|| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCATCGCCTCCTGGGTTCACGCCATT
Mismatch (t/G) at position 3

CTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCATCTGCCACCATGCCCCACTAA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCATCTGCCACCATGCCCCACTAA

ttttttctattttttAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TTTTTTCTATTTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCT

CCTGACCTCGTGATCCGCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCC
||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
CCTGACCTCCTGATCCGCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCC
Mismatch (G/C) at position 10

aTGTTTTGAGCATATAGGGAAAATTTATAAAAATTGGCCATGATGaaacataagctcaaa
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ATGTTTTGAGCATATAGGGAAAATTTATAAAAATTGGCCATGATGAAACATAAGCTCAAA

aagtttaaaaagaaaactcctaaaagttggcataacaaagcctaaaaaTCATTTCAAACT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AAGTTTAAAAAGAAAACTCCTAAAAGTTGGCATAACAAAGCCTAAAAATCATTTCAAACT

TGGTATAACTGTTACTAGAAAACCATCTACACAATGACTATATATATGCCTTTATTTCAT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGTATAACTGTTACTAGAAAACCATCTACACAATGACTATATATATGCCTTTATTTCAT

TTTTATGTTACGCTTCTCTTTATATTTGAATCATTCCTTTAAACTACATAAACATTTTCA
|||||||||| |||||||||| |||||||| |||||||||||||||||||||||||||||
TTTTATGTTAAGCTTCTCTTTCTATTTGAACCATTCCTTTAAACTACATAAACATTTTCA
Mismatch (C/A) at position 11
Mismatch (A/C) at position 22
Mismatch (T/C) at position 31

AGTGTTTGTAAATACCCTTTTAAAAATTACTGCTGTTAGCTGTTCTTCATGATTTTCTTA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AGTGTTTGTAAATACCCTTTTAAAAATTACTGCTGTTAGCTGTTCTTCATGATTTTCTTA

CTGGTCTCCTTACACATTCGAAATTGGACATTTCCGACTATTTCCTTGGTATGTTTTATA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTGGTCTCCTTACACATTCGAAATTGGACATTTCCGACTATTTCCTTGGTATGTTTTATA
[download]

I hope that's what you were looking for. :)

Update: Just realized you were looking for every mismatch rather than just the first one. Corrected.