Sophia Hyman you can try out the NCBI Multiple Sequence Alignment Viewer, provides alignment results in an interactive way just upload your data. You can export your results in a PDF file.

Sophia Hyman you can try out the NCBI Multiple Sequence Alignment Viewer, provides alignment results in an interactive way just upload your data. You can export your results in a PDF file.

If you attach the .abi original sequence files and a text file of the reference sequence it would help with what is needed to be discussed. There will be regions of poor sequencing at the start of each sequence which is normal and if the sequences are long then the end sequences will be weak and messy which is normal as well. There will also be areas at about 90 and 140 bases where dye has not been removed completely which may look wrong for 6-12 bases but are readable under the large dye peak and this is also common. Gaps are more difficult to comment on without seeing the sequences

Sophia Hyman

What exactly you were assigned, what is the actual task?

If you have performed the sanger sequencing, most probably you have to interpret

how those sequences are related. And to find that information, multiple sequence alignment (MSA) is an intermediate step. MSA followed by a phylogenetic tree construction step which will give you the information of the relatedness of the sequences.

Additionally, how did you align the sense and antisense sequences? Did you merge the sequences and then proceeded with the alignment? If not, and in the case of MSA with sense and antisense strands were aligned separately, the MSA is probably not correct or not good enough to interpret something useful. I don't know what would be the tree output from such MSA

And in case if just interpreting an alignment if the task, check this discussion

https://www.biostars.org/p/9085/