Transpositions with substitutions at the very start or end

[jkvis]

Probably these substitutions need to be lifted out of the transposition e.g.
42_43ins[CA;19_42] to [42_43insCA;ins43_44[19_42]].

ref = ATGGCGGCGGTGGTCGCCCTCTCCTTGAGGCGCCGGTTGCCGGCCACAACCCTTGGCGGA
alt = ATGGCGGCGGTGGTCGCCCTCTCCTTGAGGCGCCGGTTGCCGCACTCTCCTTGAGGCGCCGGTTGCCGGCCACAACCCTTGGCGGA