I have a list of ~200 DNA sequences, representing probably 50 different genomic regions but they're all mixed up. For example, if I have `seq1, seq2.... seq10`, `sec1` might align to `seq3` and `seq8`, but be completely unrelated to the others. There are also some differences in the lengths sampled, so the above example might represent:

`Seq1-------------------------------------------------`

`Seq3----------------------   seq8-----------------   `

Such that `seq3` and `seq8` don't align to each other, but both align to `seq1`

So what I'd like to do is go through and somehow generate a list of groups of sequences that align to each other, as well as the alignments.

Trying ClustalW or MUSSLE to align everything doesn't work (or takes an unreasonable amount of time), I'm guessing because there are so many sequences that don't align at all. I tried making a custom BLAST database and then BLASTed each sequence against it, but then I get multiple hits for the same alignment (with the example above, `seq1:seq3`, `seq1:seq8`, `seq3:seq1` and `seq8:seq1` get returned as 4 unique hits, when they should be grouped together.  

My current coding knowledge is fairly basic, but I'm willing to read docs and figure stuff out, I just don't want to reinvent the wheel.