Containing multicomponent data in rows or columns
Note: This more of a comment to help your question being answered I will delete it if needed.
It is not clear to me which analysis you want to do with this dataset thus it is hard to advice on the structure and format of the dataset.
In my experience when dealing with DNA strings and their associated features, R and in particular the Bioconductor package are the best. These packages contain already data structure, functions and operations purely design to deal with bioinformatics tasks.The GenomicAlignements could be a good start.
Hope this helps!