The present invention relates to a communication system for improved crosstalk estimation and method thereof. The communication system may include a vectoring group and a central office. The vectoring group includes a plurality of first communication lines and at least one second communication line. The plurality of first communication lines is a different type of communication line from the at least one second communication line. The central office is configured to assign the pilot sequences to each communication line within the plurality of first communication lines according to a first constraint. The central office is also configured to delay sending a sync flag in response to a request until a flag sequence of the at least one second communication line satisfies a second constraint. The assigned pilot sequences and sent flag sequences are orthogonal to each other based on the first and second constraints.