File: example.fasta

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# First gene: actA
> ST12
CGAGGAGTCCAGAAGCCTTAGCAA
> ST25
CGAGGAGTCCAGTAGCCTTAGCAA
> ST53
CGAGGAGTCCAGAAGCCTT-GCAA
=
# Second gene: recB
> ST25
CGCAGGAGTCCCAAAGAAGCCACTTAGAAACAA
> ST12
CGCAGGAGTCCCATAGAAGCCACTTAGAAACAA
> ST53
CGCAGGAGTCCC---GAAGCCACTTAGAAACAA
=
# Third gene fragment: mutX
> ST53
TGCATGCATGTGCATGCCCGAGAGCGCGATC
> ST25
-------------------------------
> ST12
TGCATGCATGTGAATGCCCGAGAGCGCGATC
=