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The main hotel website may be cheaper to book for the discount chains than even the travel sites. It may be possible to catch a weekly or monthly special that is only available through a direct booking, plus you can be put on a mailing list to receive notices of other discounts.
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If you are new to a city or area call the local Travel Bureau and ask to have a list of recommended or approved hotels emailed or sent to you directly. This can help you to determine what the quality hotels are in the area, without taking a chance with information off the web.