The fastapairs output file contains alignments in FASTA format, one
alignment for each hit (accept). Each consecutive pair of sequences
is one pair-wise alignment. Within each pair, the query is first,
then the target, with gaps inserted as needed. Here is an example
with two hits:
>Query1
CTGGGCCGTATCTCAGT-CCAATGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCAAAGCCTTGGTAAGCCA------
>Target1
CTGGGCCGTATCTCAGTCCCAATGTGGCCGGTCACCCTCTGAGGCCGGCTTCCCGTCAAAGCCTTGGTAAGCCACTACCC
>Query2
CTGGGCCGTATCTCAGTACCAATGTGGCCGGTCACCCTCT-AGGCCGGCTACCCTTGGTAAGCCACTAGG
>Target2
CTGGGCCGTATGTCAGTCCCAAT----CCGGTCACCCTCTCAGGCCGGCTAGCCTTGGTAAGCCACTAC-
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