Different Patterns on Different Agaroses.... - ...Why? (May/20/2008 )

My guess is differences in the agarose (for example different impurities for each type), will lead to slight differences in the cross linking during gelification, which results in differences in the pores size and therefore a minor, yet noticeable, change in the pattern of the bands.
Not sure is that of course, just an idea.

Different agaroses are going to have different sieving properties. It’s not surprising that the two gels show slightly different banding patterns. I would be interested to know which agarose separated the fragments better (i.e. band sizing is closest to the true value). I suspect MetaPhor Agarose preformed better. The answer is easy now, since you are comparing MetaPhor Agarose to an inferior product you are bound to see a difference. That difference is the Invitrogen agarose standard error.

Unfortunately, we do not know the exact chemical composition of MetaPhor agarose. The Ararose 1000 composition is proprietary. It may be that the capacity to separate fragments in the intermediate size range is better with Agarose 1000. There seems to be one additional band which is not present in the MetaPhor gel. In-house we have determined that Agarose 1000 has generally superior separation characteristics compared to MetaPhor.