#!/usr/bin/perl
use warnings;
use strict;
use feature qw{ say };

my $small_str = 'AAATTGGTGTATATGAAAGACCTCGACGCTATTTAGAAAGAGAGAGCAATATTTCAAGAAT'
    . 'GCATGCGTCAATTTTACGCAGACTATCTTTCTAGGGTTAAATATACTGACAGTGTGCAGTGACTCACAAAA'
    . 'GATGATTA';
my $reference_str = 'ACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGG'
    . 'GGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACGTCCATACTGAGAATCA'
    . 'TGTTAACATTAGTGGGTGCAGCGCACAAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGC'
    . 'ACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAAAACACATTAAAAAAAAAA'
    . 'AAAACAACAAAACAAAGCAAACATGGAAATGTTTGTTATTTTAATTGTTATGATGGTTTCATGGCTGTTTG'
    . 'CATGTGTCAAAACTCATCAAATTTGTGTACGTTAAATATGTGAAACTTATTGTATGCTGGTTACACCTCAA'
    . 'TAAAGCTGTTAAATTTAAAAAAAAAAAAAAAAAAAAAAATCACCAATAGTTGCTGCTAGAAATCCAGTGTC'
    . 'ACAAAAGGCCAAAGTTTATTGACAAATTGGTGTATATGAAAGACCTCGACGCTATTTAGAAAGAGAGAGCA'
    . 'ATATTTCAAGAATGCATGCGTCAATTTTACGCAGACTATCTTTCTAGGGTTAATCTAGCTGCATCAGGATC'
    . 'ATATCGTCGGGTCTTTTTTCCGGCTCAGTCATCGCCCAAGCTGGCGCTATCTGGGCATCGGGGAGGAAGAA'
    . 'GCCCGTGCCTTTTCCCGCGAGGTTGAAGCGGCATGGAAAGAGTTTGCCGAGGATGACTGCTGCTGCATTGA'
    . 'CGTTGAGCGAAAACGCACGTTTACCATGATGATTCGGGAAGGTGTGGCCATGCACGCCTTTAACGGTGAAC'
    . 'TGTTCGTTCAGGCCACCTGGGATACCAGTTCGTCGCGGCTTTTCCGGACACAGTTCCGGATGGTCAGCCCG'
    . 'AAGCGCATCAGCAACCCGAACAATACCGGCGACAGCCGGAACTGCCGTGCCGGTGTGCAGATTAATGACAG'
    . 'CGGTGCGGCGCTGGGATATTACGTCAGCGAGGACGGGTATCCTGGCTGGATGCCGCAGAAATGGACATGGA'
    . 'TACCCCGTGAGTTACCCGGCGGGCGCGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTT'
    . 'ATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTG'
    . 'AGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCA'
    . 'TTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTG'
    . 'ACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCC'
    . 'ACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAA'
    . 'GGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTC'
    . 'AGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCT'
    . 'CCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCA'
    . 'TAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCC'
    . 'CCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTA'
    . 'TCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTT'
    . 'GAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTA'
    . 'CCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTT'
    . 'TGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGA'
    . 'CGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGA'
    . 'TCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTAC'
    . 'CAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCC'
    . 'CGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACC'
    . 'CACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCT'
    . 'GCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAA'
    . 'TAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCAT'
    . 'TCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCC'
    . 'TTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCA'
    . 'TAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCT'
    . 'GAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGC'
    . 'AGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTT'
    . 'GAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTT'
    . 'CTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAAAAGGGCGACACGGAAATGTTGAATAC'
    . 'TCAT';

for my $start_pos (0 .. length($reference_str) - 11) {
    my $xor = $small_str ^ substr $reference_str, $start_pos, length($reference_str) - 1;
    for my $inner_pos (0 .. length($xor) - 10) {
        if (9 <= substr($xor, $inner_pos, 10) =~ tr/\0//) {

            say $start_pos + $inner_pos;
            say substr $small_str, $inner_pos, 10;
            say substr $reference_str, $start_pos + $inner_pos, 10;

        }
    }
}


##</code><code>##

my $stretch = 10;
my $mismatches = 1;

substr $reference_str, 0, 0, 'x' x (length($small_str) - 1);
$reference_str .= 'x' x (length($small_str) - 1);

for my $start_pos (0 .. length($reference_str) - 1 - $stretch) {
    my $substr = substr $reference_str, $start_pos, length($small_str) - 1;
    my $xor = $small_str ^ $substr;
    for my $inner_pos (0 .. length($xor) - $stretch) {
        if ($stretch - $mismatches <= substr($xor, $inner_pos, $stretch) =~ tr/\0//) {
            my $match = substr $reference_str, $start_pos + $inner_pos, $stretch;
            next unless -1 == index $match, 'x';

            say $start_pos + $inner_pos + 1 - length $small_str;
            say substr $small_str, $inner_pos, $stretch;
            say $match;
        }
    }
}


##</code><code>##

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,