This is a great time for regular expressions! The commands are very similar in bash scripting as well, so it's a useful tool to learn.
%input string
str = '123345KR00994;#3;#160225MD0004;#2;#13161504900013;#1';
%split string in to cell array by delimiter ';#'
t = regexp(str,';#','split');
%put alphanumeric values along first row, order along second row
t = reshape(t,2,length(t)/2);
alphanumeric = t(1,:);
%convert order to array of numbers
indices = str2double(t(2,:));
%order alphanumeric values properly (already ordered in example string...)
alphanumeric = alphanumeric(length(alphanumeric) - indices + 1);
