Phylogenetic Tree- full ITS v. partial ITS

Question

I hope to make a single phylogenetic tree by comparing reads that cover ITS 1 or ITS 2 to reads that cover both regions (ITS1&2). (details: similar fungi, ITS region, Sanger reads of ~600bp) Is there a program/technique to compare partial reads to a full read and not have the tree group by primer?

Drawing: Line is where the primer covers and I hope to compare the partial lines (3-6) to the full line (1-2).

1. _________.
2. _________.
3. _____........
4. _____........
5. ....... _____.
6. ....... _____.

Here is an image of the alignment: