When shooting Macro (I have a Canon 100mm) I always use manual focus. Especially at shallow depth of field. Quite often auto-focus will not focus on the exact spot you wish it to.
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Canon Rebel XSI
EF-S 17-85mm f/4-5.6 IS USM
EF 70-300mm f/4.5-5.6 DO IS USM
EF 100mm f/2.8 Macro USM
EF 50mm f/1.8 II
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