I have a large number of reads from sequences that were generated by randomly shuffling regions of two parent sequences together. See the following image:
The regions that are shuffled are around 100-200 bp in length. The full shuffled sequence is around 1000 bp long. In general, the regions will be in the same order as the original sequence. The shuffled sequences are fragmented and sequenced into 150bp reads. One read can contain more than two borders between shuffle regions from a different parent sequence.
The sequences are very similar (95%). Because of this high similarity you cannot pinpoint the border between two regions. The border will be a range between a variant that is unique to source1 and a variant that is unique to source2. That is ok because I am not interested in knowing from which source an identical region came.
I would like to identify which part of the read originates from parent sequence one or two. What would be a suitable tool to do this?
I tried to look at some multiple sequence alignment tools like MAFFT or Clustal but I am not interested in aligning all reads to each other. They also don't identify the shuffle regions well in my testing.