Karishma, The problem is you're trying to combine map coordinates with unprojected coordinates. Either is fine to use, but they won't work together. The distinction is that the Mapping Toolbox converts (lat,long) coordinates into projected values that are usually in the range of -0.5 to 0.5, so if you plot that with lats and longs that are tens to hundreds of degrees, things won't line up. Here's one option that uses unprojected coordinates. After your loop do this:
% Plot your data:
plot(long, lat,'r.');
xlabel('Longitude')
ylabel('Latitude')
% Load and plot coastline data:
C = load('coast.mat');
plot(C.long,C.lat,'b')
borders('continental us','b','NoMappingToolbox')
If you want to use the Mappig Toolbox you can do:
usamap(latlim, lonlim)
plotm(lat,long)
Note, above I used plotm instead of plot.
