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In real-time towed-array systems, performance degradation of array gain occurs when a line array that is not straight is assumed straight in the beamforming process. In this paper, a new method is proposed for array shape estimation. The novelty of this method is that it accounts for the variations in the tow ship's speed, which are typical during course alterations. The procedure consists of two steps. First, we solve for the tow-point induced motion in the time domain based on the constraints from the tow-point compass-sensor readings and from a discretized Paidoussis equation. At each time instance, the shape estimate is solved from a linear system of equations. We also show that this solution is equivalent to a previous frequency-domain solution while the new approach is much simpler. In the second step, we use the tail compass-sensor data to adjust the overall array shape. By noting that variations in the ship speed lead to a distortion in the normalized time axis, we first register the predicted tail displacement with the tail sensor readings along the time axis. Then, distortions in the estimated array shape over its length can be compensated accordingly. We also model a slow-changing bias between sensor zeros and remove systematic sensor errors. The effectiveness of the new algorithm is demonstrated with simulations and real sea-trial data.