This is quick made example how it may work. Nbest tells number of letters in the longest string and Lbest tells what letters the string consists of
clear;clc;close all;
str='AAATTTTTCCCCCAATTCCC';
AGTCstr='AGTC';
Strsize=size(str);
AGTCsize=size(AGTCstr);
temp=0;
k=0;
Nbest=0;
for i=1:Strsize(2)
for j=1:AGTCsize(2)
h=strcmp(str(i),AGTCstr(j));
if h==0
continue
end
if h==1
k=k+1;
if strcmp(temp,str(i))==0
if k>=Nbest
Nbest=k;
Lbest=temp;
end
k=0;
end
temp=str(i);
end
end
end
