Yes, that example doesn't match at all. I just write some atcg letters to put as an example. The matching was done previously, and now I am interested in formatting the results I had previusly.

The important thing here is that each substring should vertically match with the reference string, in the position that I have previously stored. Each of the substrings is one result: in this example, the line out1 have 3 different substrings, and out2 and out3 have one each (they are in different lines because they are overlapped).