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#!/usr/bin/perl
use strict;
use warnings;
...
Name_3    PA    PA_6336
Name_4    TT    XL_928294.1
Name_4    PA    PA_917

PA              TT          AT
PA_392          XL_927799.1 ZX_003039195.1
                XL_931313.1 ZX_003043016.1
PA_5040,PA_6336 XL_929616.1
PA_917          XL_928294.1