it is usually possible to sequence indels. you sequence from both ends and the sequences start clean and good then at the indel there are 2 sequences so it looks messy. If you know the correct sequence then each position after the clean sequence you subtract the known sequence base and the remaining base is the next base after the indel.when you have a few bases then for short indels it becomes obvious where they fit into the known sequence. Cloning and sequencing clones will give both sequences separately to confirm the change