How can I calculate aligned sequence length coverage from the results of protein domains obtained through pfam_scan.pl program. The result consist of columns such as

input seqs_id

alignment start and end

envelope start and end

hmm_accession

hmm_name

type

hmm start and end (I don't know)

hmm length

bit score

E-value

significance

I am trying to calculate the aligned sequence length coverage for each protein and filter the results. Could anyone please suggest me how can I calculate the same