lucy(perky):~/src/chk% cat test1.fasta
>test1
AAAGTCAGTCAGTCAA
AAAGTCAGTCAGTCAA
>test3
AAAGTCAGACAGTCAA
AAAGTCAGTCAGTCAA
>test4
AAAGTCAGTCAGTCAT
AAAGTCAGTCAGTCAA
lucy(perky):~/src/chk% echo blast -p blastn -i test1.fasta -j test1.fasta -B1
blast -p blastn -i test1.fasta -j test1.fasta -B1
lucy(perky):~/src/chk% blast -p blastn -i test1.fasta -j test1.fasta -B1
# BLASTN 2.2.13 [Nov-27-2005]
# Query: 3 sequences
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
test3   Unknown 96.88   32      1       0       1       32      1       32      1e-14  56.0
test4   Unknown 96.88   32      1       0       1       32      1       32      1e-14  56.0
test3   Unknown 100.00  32      0       0       1       32      1       32      4e-17  63.9
test4   Unknown 93.75   32      2       0       1       32      1       32      3e-12  48.1
test4   Unknown 100.00  32      0       0       1       32      1       32      4e-17  63.9
test3   Unknown 93.75   32      2       0       1       32      1       32      3e-12  48.1