Analyzing 2 Different Time Block Arrays

This is slightly similar to the questions I asked earlier about comparing a "tooth" to a "box" to find where they line up. Well, instead of doing that, now I want to compare one box array to another box array. The first box array consists of 2 arrays of the same size called startA & FinishA, and second box array consists of 2 arrays of the same size called startB & FinishB . The "A" arrays need to be lined up with the "B" arrays as best as possible by finding the best offset that is added to the "B" arrays, which is, at most, 1/3 the size of box arrays "A".

Here is the code that does work when B is a "tooth" and not a box:

    CPIncrement = TimeB; %reset CPIncrement to default
    offset = double.empty;
    percent = double.empty;
    tickcount = double.empty;
    tick = 0;
    percentCalc = 0;
    Filtersize = numel(startTimeA);
    CPsize = numel(TimeB);
    Offsets = combStart : 0.000001 : combFinish;
    IncrementInstances = numel(Offsets);
    toothCount=zeros(numel(CPIncrement), IncrementInstances);
    toothColumn=1;
    for b = Offsets
        tic;
        CPIncrement = TimeB+b;
        disp(['Offset = ', num2str(b)]);
        for i = 1:Filtersize
            if (  any(CPIncrement >= startTimeA(i) & CPIncrement <= finishTimeA(i))   )
            %see if a value of A falls within B and its life
            %if it does, add a tick to be used as a percentage later
                clear tmpVec;
                tmpVec=CPIncrement >= NoDupFilterTime(i) & CPIncrement <= NoDupFilterLife(i);
                toothCount(tmpVec==1, toothColumn) = toothCount(tmpVec == 1, toothColumn) + 1;
            end
        end
        disp(['ticks = ', num2str(tick)]);
        tick=sum(numel(find(toothCount(:,toothColumn)~=0)));
        tickcount(end+1) = tick;
        %tickcount = [tickcount; tick];
        percentCalc = tick/CPsize*100.0;
        %calculate the precentage
        disp(['percent = ', num2str(percentCalc)]);
        toothColumn=toothColumn+1;
        offset(end+1)= b; %adds an additional element of the offset "a" to the growing vector of "offset" to be used for later comparison
        %offset = [offset; b] % Legacy version, column vector format
        percent(end+1)= percentCalc; %does same thing as previous line.
        %percent = [percent; percentCalc] %Legacy version, column vector format
        percentCalc = 0; %reset percentCalc
        disp(['percent reset = ', num2str(percentCalc)]);
        toc;
    end