This is a bit complicated but I'm hitting a wall, so please bear with me...

I have written a perl script for searching a reference database with a ~30 base probe. I'm trying to expand it to allow a defined number of mismatches and this led me to String::approx.

The modifiers in the 'aindex' command allow you to define numbers of Insertions, Deletions and Substitutions (Ix,Dx,Sx). If I have these as I0,D0,S0 then I get exact matching as expected but if I use I0,D0,S1 then it matches significantly more than one substitution and I cant understand why

Relevant code snippet:

while (my $seq = $in->next_seq()){
        my $ref = $seq->seq;
        my $new_id = $seq->display_id;

         foreach my $pr (@seqarray){
                my $index = aindex($pr, ["I0","D0","S1"], $ref);
                if ($index != -1){
                        my $match = substr($ref, $index, 30);
                        print "$new_id\t$index\t$match\n";
                        last;
                }
        }

Defining the modifiers as ["I0","D0","S0"] I get:

Species_header    match_position   matching_sequence</code>

<code>Cryptosporidium_15318   813     TAGGGACAGTTGGGGGCATTTGTATTTAAC
Cryptosporidium_67285    820     TAGGGACAGTTGGGGGCATTTGTATTTAAC
Cryptosporidium_80642    822     TAGGGACAGTTGGGGGCATTTGTATTTAAC
Cryptosporidium_86835    822     TAGGGACAGTTGGGGGCATTTGTATTTAAC</code>

Defining the modifiers as ["I0","D0","S1"] I get:

<code>Eimeria_10865  51              TGTGTTTATTAGGTACAAAACCAACCCACT
Hepatozoon_12528    866         TAGGGACAGTTGGGGGCATTTGTATTTAAC
Cryptosporidium_15318    809    TTAATAGGGACAGTTGGGGGCATTTGTATT
Cryptosporidium_34679    842    TATTTAACAGCCAGAGGTGAAATTCTTAGA
Hepatozoon_54015    844         TAGGGACAGTTGGGGGCATTTGTATTTAAC

These matching sequences are real, and in the reference fasta file, but I don't understand how allowing one substitution is causing this. If anyone has any experience with this I would greatly appreciate it! I have seen the solution that Kenosis gave to Perl :Fuzzy Matching Problem which I might try to implement, but I really want to work out why this is causing such unusual results.

Thanks

UPDATE:

So it looks like changing [S0] to [S1] is causing a 4 character offset. This is what I get when changing nothing but the [S1]:

I think it must be the index being incorrectly defined under substitution conditions. Here's the data for Eimeria_10865

---------Zero Substitutions [S0]
probe: TAGGGACAGTTGGGGGCATTTGTATTTAACT
match: TAGGGACAGTTGGGGGCATTTGTATTTAACT

----------One Substitution [S1]
probe: TAGGGACAGTTGGGGGCATTTGTATTTAACT
match: TTAATAGGGACAGTTGGGGGCATTTGTATTT

Eukaryota;Alveolata;Apicomplexa;Coccidia;Eucoccidiorida;Eimeriorina;Eimeriidae;Eimeria;;Eimeria_10865:
TGGTTATTCTACGGCTAATATGTGCGCAATGGCCTCCTTCTCTGGAGGGGCTGTGTTTATTAGGTACAAAACCAACCCACTTTGGTGGACTCTTGGTGATTCATAGTAACCGAACAGATCGCAATTGGCTTGTTGTGGGCACGTTCGATTCCGGAGAGGGAAGCTGAGAAACGGCTACCACATCTAAGGAAGGCAGCAGGCGCGCAAATTACCCAATGAAAACAGTTTCGAGGTAGTGACGAGGAATAACAGTACAGGGCATTTTTTGCTCTGTAATTGGAGTAATGCGAATGRAAGACCCTTTCAGAGTAACAATTGGAGGGCACGTCTGGTGCCCGCAGCCGCTGTAGTTCCAGCTCCAATAGTGCACATTAGAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTCGTGGTCATCCGGTCGCCCGTATGGGTGTGTGCCTGGTATGACCGCGGCTTTCCTCTGGTAGCCAGCCATCCGCGCTTAATTGCGTGTGTTGGTGTTGAACTAGGACTTTTACTTTGAGAAAAATAGACTGTTTCAAGCAGGCTGGTCGTCCTGAATACTTCAGCATGGAATATGAGGATAGAACCTCGGTTTTATTTTGTTGGTTTTTGGGACCAAGGTATTGATTAATAGGGACAGTTGGGGGCATTTGTATTTAACTGTCAGAGGTGAATTTCTTAGATTTGTTAAAGACGAACTACTGCGACACCATTTGCCAAGGAAGTTTTCATTAATCAAGAACGGTAGCAGGGGGTTCGAGGACGATTAGGCACCGTCGTAATCTCTACCATAAACTATGCGGACTACAGATAGGGAAATGCCTATCTTGGCTTCTCCTGCACCTCATGAGAAGTCGAAGTCTTTGGGTTCTGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAGTTGACGAAAGGGCACCACCAGGCCTGGAGCCTGCGGCTTAATTTGACTCCACACGCGGGAACTCACCAGGTCCAGACATGGGAAGGATCGACAGATTGATAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCAGTTTTTAGTTGGTGGAGTGACCTGTCTGGTGAATTTCGATAACGAACGAGACCTTAGCCTGCTTAATAGGATCAAGAACCTCGATTCTCGTATCACTTTATAGAGGGACTTTGCGTGTCCAACGCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTCAGATGTTCTGTGCTGCACACGCGCTACATTGATGCATGCAACGAGCTTTTGACCTTGGCCGACAGGTCTAGGTAATCTTTTGAGTATGCATCGTGATGGGGGTAGAATATTGCAACTATTAATCT