[BioC] Biostring: print sequence alignment to file

[Martin Preusse]

I do a simple pairwise DNA sequence alignment with pairwiseAlignment from the Biostrings package in Bioconductor:

library('Biostrings')
seq1 = 'ATGCTA'
seq2 = 'ATGTA'
pairwiseAlignment(pattern = seq1, subject = seq2)

The output looks as follows:

Global PairwiseAlignedFixedSubject (1 of 1)
pattern: [1] ATGCTA 
subject: [1] ATG-TA 
score: -4.091219 

For very long sequences, the output is truncated and only one line is shown:

Global PairwiseAlignedFixedSubject (1 of 1)
pattern: [1] AT-----------------------------...----------------TGTCTTCCAKATCTGGCGCGCCTGGGTTGATATC 
subject: [1] ATTGGCGGCCGCGCCACCATGCCAGAGCCAG...GAAGGCTGTATGCTGTTGTCTTCAAGATCTGGTACCGCTGGGTTGATATC 
score: -29418.8

How can I output the complete alignment to a text file?

Cheers,
Martin