Some index utils in List:MoreUtils are useful;

use strict;
use warnings;
use List::MoreUtils qw(firstidx indexes);
use Data::Dump qw(pp);

my @matrix = (
    [qw(t1 t1 t2 t2 t2)], 
    [qw(a1 a2 a1 a1 a2)], 
    [qw(intron intron UTR_CG UTR UTR)], 
);


die "No UTR_CG column!" unless ( (firstidx {$_ eq 'UTR_CG'}@{$matrix[-
+1]}) > -1);

my @utr_cols = indexes { $_ eq 'UTR' } @{$matrix[-1]};

die "Must have 2 or more UTR columns!" unless (@utr_cols >= 2);

shift @utr_cols; #save first seen UTR column
delete @{$matrix[$_]}[@utr_cols] for (0..@matrix-1);

pp \@matrix;

__END__
[
  ["t1", "t1", "t2", "t2"],
  ["a1", "a2", "a1", "a1"],
  ["intron", "intron", "UTR_CG", "UTR"],
]
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