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ladderpEXPR TRE:SykhEF1a:CymRhEF1a-CuO:mKateCMV5-CuO:mKate 
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  goodgoodWeird gel is geneious file aligned with gel.  The ladders are  lined up at 1 and 3 kb, the virtual bands are in the correct places relative to the virtual ladder.  This has an extra band but it is probably ok I guess.