That there are a differing number of entries per day makes it a little more of a challenge; that they kindly gave you the count instead of having to find out that number is a boon...
fid=fopen('lat_econtent.txt','rt'); % open file
da=fscanf(fid,'%d',3); % get first date
nDay=365+isleapyr(d(1)); % how many days in this year
eMax=zeros(nDay,2); % allocate space for that many
frewind(fid) % reposition to get clean start to loop
for i=1:nDay
da=fscanf(fid,'%d',3); % get first date
n=fscanf(fid,'%d',1); % get number observations for day
dat=cell2mat(textscan(fid,'',n)); % scan that many
[~,ix]=max(dat(:,2)); % find max location
eMax(i,:)=dat(ix,:); % get lat and max for first
end
fid=fclose(fid);
The result of the above here produced via
>> emax
>> subplot(2,1,1)
>> plot(1:length(eMax),eMax(:,2))
>> subplot(2,1,2)
>> plot(1:length(eMax),eMax(:,1))
NB: I included the location as well as the max; figured it would be the obvious next step despite your not having asked for it... :)
ADDENDUM
You don't need any additional variable for DOY; it's the same as the sequential storage location, 1:nDay.
Oh, and isleapyr is a one-liner utility routine --
function is=isleapyr(yr)
% returns T for input year being a leapyear
is=eomday(yr,2)==29;
