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Accurate Shape-estimation for a large-aperture bottom-mounted array in shallow water is required for the target detection, which is often degraded by the channel dispersion and asynchronous clock. A shape estimation method is proposed for a large-aperture bottom-mounted array whose elements are loosely synchronized in time. The low-frequency active emissions, which excite only the first order normal modes in the waveguide, are used as the calibration signals. The phase velocity across the frequency band is calculated based on the channel parameters, and used to eliminate the negative influence of the modal dispersion. With the GPS information of the sources and the reference array element, the element positions as well as their clock offsets are estimated. The experimental data are used to demonstrate the superior performance of the proposed method for the array shape and clock offset estimation for various parameter-mismatched scenarios. The results on real data collected at sea with a 860-m-long array with 15 sensors demonstrate that the accuracy of the direction-of-arrival estimation and the array gain are improved by 0.2゜ and 1.8dB for the broadside targets, 0.4゜ and 4.4dB for the end-fire targets respectively.