If i'm correct in my understanding of your data, it looks like you want to take the first and fifth line of data for every 5 lines in your text file.
You could try reading the text file line by line using fgetl(). This returns the next line of your file as a character vector, then use str2num() to convert your character vector to a 1x2 array in this case. I've added in conditions to store only the lines you specified. Note that you need to have waterscape2.txt in your current working directory or else filename has to be changed, for example filename='C:\...\waterscape2.txt'.
fid = fopen(filename);
c=0; ij=; DxDy=;
tline = fgetl(fid);
Aside from fgetl there is also some relevant documentation here for reading data line-by-line.