DNA comparison: Repeated-measures ANOVA.. but too many parameters to consider?

Dilemma about which test to correctly use... It's a tricky, confusing, one!
I'm looking at DNA extraction methods, here's how I've got the data set up:
Genotyped data from 80 fish, using 14 markers.
So, for each fish, for 14 markers, theres two paired values per marker (2 alleles).

However: then used 4 different methods of extraction on each fish to compare for quality.

So, for each individual fish, there are 4 rows of data for each method... with each row having 14 markers of paired values.

Anyone with me so far?

Basically, I want to look to see if there are any differences between the values for each method.... I'm thinking repeated-measures ANOVA, but trying to take into account the paired values for so many different markers, with different methods, for different fish is tricky...

Any suggestions on a test? I'm desperate and at my wits end trying different combinations.
Plee for help :confused: