If you want to keep using numeric matrices:
[~, whereinA] = ismember(B(:, [2 4 6]), A(:, 1))
C = reshape([reshape(B.', 2, []); A(whereinA, 4).'], 9, []).'
However, you may want to switch to tables since all your columns seem to represent different things:
A = [1,3.43,2.34,5.43,3.22;
2,8.32,6.34,7.34,2.34;
3,3.67,8.34,8.23,1.34;
4,2.67,6.89,4.99,8.65;
5,1.33,5.42,2.53,6.13];
B = [ 0.12,2,0.15,1,0.65,3;
0.33,5,0.62,4,0.55,1;
0.91,1,0.77,2,0.66,5];
tA = array2table(A, 'VariableNames', {'Sample', 'SomeProp', 'OtherProp', 'Prop3', 'LastProp'})
tB = array2table(B, 'VariableNames', {'StartValue', 'StartSample', 'MidValue', 'MidSample', 'EndValue', 'EndSample'})
tC = tB;
for samp = 1:3
tC = join(tC, tA, 'LeftKeys', tB.Properties.VariableNames{samp*2}, 'RightKeys', 'Sample', 'RightVariables', 'Prop3');
end
tc.Properties.VariableNames(end-2:end) = {'StartProp3', 'MidProp3', 'EndProp3'};
it may be longer, but make it clearer what is happening and you end up with output that is more readable.
