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Phrase alignment is a crucial step in phrase-based statistical machine translation. We explore a way of improving phrase alignment by adding syntactic information in the form of chunks as soft constraints guided by an in-depth and detailed analysis on a hand-aligned data set. We extend a probabilistic phrase alignment model that extracts phrase pairs by optimizing phrase pair boundaries over the sentence pair [1]. The boundaries of the target phrase are chosen such that the overall sentence alignment probability is optimal. Viterbi alignment information is also added in the extended model with a view of improving phrase alignment. We extract phrase pairs using a relatively larger number of features which are discriminatively trained using a large-margin online learning algorithm, i.e., Margin Infused Relaxed Algorithm (MIRA) and integrate it in our approach. Initial experiments show improvements in both phrase alignment and translation quality for Arabic-English on a moderate-size translation task.