Iterate over the possible positions in the longer string. Use XOR to get a string that contains zero bytes in positions where two strings are the same. Then just use tr to count the number of zeroes in substrings of length 10, report the positions if the number is 9 or 10. 
#!/usr/bin/perl
use warnings;
use strict;
use feature qw{ say };

my $small_str = 'AAATTGGTGTATATGAAAGACCTCGACGCTATTTAGAAAGAGAGAGCAATATT
+TCAAGAAT'
    . 'GCATGCGTCAATTTTACGCAGACTATCTTTCTAGGGTTAAATATACTGACAGTGTGCAGTGAC
+TCACAAAA'
    . 'GATGATTA';
my $reference_str = 'ACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGAC
+TGTGGTGG'
    . 'GGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACGTCCATACT
+GAGAATCA'
    . 'TGTTAACATTAGTGGGTGCAGCGCACAAGCATGGCACATGTATACATATGTAACTAACCTGCA
+CAATGTGC'
    . 'ACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAAAACACATTAA
+AAAAAAAA'
    . 'AAAACAACAAAACAAAGCAAACATGGAAATGTTTGTTATTTTAATTGTTATGATGGTTTCATG
+GCTGTTTG'
    . 'CATGTGTCAAAACTCATCAAATTTGTGTACGTTAAATATGTGAAACTTATTGTATGCTGGTTA
+CACCTCAA'
    . 'TAAAGCTGTTAAATTTAAAAAAAAAAAAAAAAAAAAAAATCACCAATAGTTGCTGCTAGAAAT
+CCAGTGTC'
    . 'ACAAAAGGCCAAAGTTTATTGACAAATTGGTGTATATGAAAGACCTCGACGCTATTTAGAAAG
+AGAGAGCA'
    . 'ATATTTCAAGAATGCATGCGTCAATTTTACGCAGACTATCTTTCTAGGGTTAATCTAGCTGCA
+TCAGGATC'
    . 'ATATCGTCGGGTCTTTTTTCCGGCTCAGTCATCGCCCAAGCTGGCGCTATCTGGGCATCGGGG
+AGGAAGAA'
    . 'GCCCGTGCCTTTTCCCGCGAGGTTGAAGCGGCATGGAAAGAGTTTGCCGAGGATGACTGCTGC
+TGCATTGA'
    . 'CGTTGAGCGAAAACGCACGTTTACCATGATGATTCGGGAAGGTGTGGCCATGCACGCCTTTAA
+CGGTGAAC'
    . 'TGTTCGTTCAGGCCACCTGGGATACCAGTTCGTCGCGGCTTTTCCGGACACAGTTCCGGATGG
+TCAGCCCG'
    . 'AAGCGCATCAGCAACCCGAACAATACCGGCGACAGCCGGAACTGCCGTGCCGGTGTGCAGATT
+AATGACAG'
    . 'CGGTGCGGCGCTGGGATATTACGTCAGCGAGGACGGGTATCCTGGCTGGATGCCGCAGAAATG
+GACATGGA'
    . 'TACCCCGTGAGTTACCCGGCGGGCGCGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG
+AAATTGTT'
    . 'ATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCT
+AATGAGTG'
    . 'AGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGC
+CAGCTGCA'
    . 'TTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTC
+GCTCACTG'
    . 'ACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATAC
+GGTTATCC'
    . 'ACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAAC
+CGTAAAAA'
    . 'GGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACG
+CTCAAGTC'
    . 'AGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCG
+TGCGCTCT'
    . 'CCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCG
+CTTTCTCA'
    . 'TAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCA
+CGAACCCC'
    . 'CCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGAC
+ACGACTTA'
    . 'TCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACA
+GAGTTCTT'
    . 'GAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAA
+GCCAGTTA'
    . 'CCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTT
+TTTTTGTT'
    . 'TGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACG
+GGGTCTGA'
    . 'CGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTT
+CACCTAGA'
    . 'TCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTG
+ACAGTTAC'
    . 'CAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCC
+TGACTCCC'
    . 'CGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACC
+GCGAGACC'
    . 'CACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAA
+GTGGTCCT'
    . 'GCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCG
+CCAGTTAA'
    . 'TAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTAT
+GGCTTCAT'
    . 'TCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGG
+TTAGCTCC'
    . 'TTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCA
+GCACTGCA'
    . 'TAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAA
+GTCATTCT'
    . 'GAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGC
+CACATAGC'
    . 'AGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTA
+CCGCTGTT'
    . 'GAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCAC
+CAGCGTTT'
    . 'CTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAAAAGGGCGACACGGAAATG
+TTGAATAC'
    . '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;

        }
    }
}

[download]

TODO: Handle matches where the two strings don't fully overlap.

Update Probably like this? It wraps the longer string in characters that can never match, so some simple math is needed to get the original position back:

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, $stretc
+h) =~ 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;
        }
    }
}

[download]

($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,

[download]

In reply to Re: How do you match a stretch of at least N characters by choroba
in thread How do you match a stretch of at least N characters by Anonymous Monk

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