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#!perl -slw
use strict;
...
chrM:309    2    TCAGGGTG    130
chrM:309    2    TCAGGGTG    129

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C:\code\perlmonks>perl pm_1198131.pl
CLUSTER
...
chrM:309        1       TCAGGGTG        106
chrM:309        2       TCAGGGTG        129
chrM:309        2       TCAGGGTG        130