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AliBaba 2 - prediction of transcription factor binding sites by context dependent matrices generated from TRANSFAC 3.5 public sites.
http://www.alibaba2.com/

MatInspector professional is a tool that utilizes a library of matrix descriptions for transcription factor binding sites to locate matches in sequences of unlimited length (free of charge for academic).
http://www.genomatix.de/software_services/software/MatInspector/matinspector.html