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#!/usr/bin/perl -w
use strict;
...
    print @a, "\n", @b, "\n", @c, "\n";
    print $mm ? "$mm\n" : "\n";
}

TGtAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCATCGCCTCCTGGGTTCACGCCATT
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...
CTGGTCTCCTTACACATTCGAAATTGGACATTTCCGACTATTTCCTTGGTATGTTTTATA
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CTGGTCTCCTTACACATTCGAAATTGGACATTTCCGACTATTTCCTTGGTATGTTTTATA