printPairwiseAlignment <- function(alignment, chunksize = 60, returnlist = FALSE)
  {
     require(Biostrings)           # This function requires the Biostrings package
     seq1aln <- pattern(alignment) # Get the alignment for the first sequence
     seq2aln <- subject(alignment) # Get the alignment for the second sequence
     alnlen  <- nchar(seq1aln)     # Find the number of columns in the alignment
     starts  <- seq(1, alnlen, by = chunksize)
     n       <- length(starts)
     seq1alnresidues <- 0
     seq2alnresidues <- 0
     for (i in 1:n) {
        chunkseq1aln <- substring(seq1aln, starts[i], starts[i] + chunksize-1)
        chunkseq2aln <- substring(seq2aln, starts[i], starts[i] + chunksize-1)
        # Find out how many gaps there are in chunkseq1aln:
        gaps1 <- countPattern("-",chunkseq1aln) # countPattern() is from Biostrings package
        # Find out how many gaps there are in chunkseq2aln:
        gaps2 <- countPattern("-",chunkseq2aln) # countPattern() is from Biostrings package
        # Calculate how many residues of the first sequence we have printed so far in the alignment:
        seq1alnresidues <- seq1alnresidues + chunksize - gaps1
        # Calculate how many residues of the second sequence we have printed so far in the alignment:
        seq2alnresidues <- seq2alnresidues + chunksize - gaps2
        if (returnlist == 'FALSE')
        {
           print(paste(chunkseq1aln, seq1alnresidues))
           print(paste(chunkseq2aln, seq2alnresidues))
           print(paste(' '))
        }
     }
     if (returnlist == 'TRUE')
     {
        vector1 <- s2c(substring(seq1aln, 1, nchar(seq1aln)))
        vector2 <- s2c(substring(seq2aln, 1, nchar(seq2aln)))
        mylist <- list(vector1, vector2)
        return(mylist)
     }
}