llele: any of the alternative forms of a gene that may occur at a given locus."source: Merriam-Webster Medical Dictionary, © 2002 Merriam-Webster, Inc. per dictionary.com". 

An analogy that might make the concept of genetics more tangible and easier to understand is a printed encyclopedia set.  Basically, genetic code is a complex recipe for how to make a living thing.  It's so long that it's divided into separate chromosomes that could be thought of as the volumes for each letter of an encyclopedia set (A-Z).  Each gene could be thought of as a page with it's locus as the combination of volume letter and page number.  The recipe is so important that you have two full encyclopedia sets (and hence two copies of every gene/volume+page combination), one encyclopedia set from your mother and one from your father.  The exception from having two copies of each volume is the gender chromosome/volume where female snakes have an unmatched pair (w from mother and z from father) and males have a matched pair (zz -  one from each parent).

A mutation is basically a copy error in a page, probably started long ago and passed down.  Alleles are two different mutations of the same gene (think two different copy errors of the same page in the same volume).  They probably happened completely independently at different times but later we crossed them and figure out that they are on the same page and that they are alleles rather than just unrelated mutations of different genes.  Say for example that it turns out that a missing paragraph on page 200 of volume B is the albino mutation.  What if there was a separate mutation also of page 200 of volume B?  Maybe instead of the missing paragraph this one just has a misspelled word with two letters switched.  Instead of making an albino this mutation might create a caramel.

If these two mutations where alleles then a homozygous albino would have two copies of volume B page 200 both missing the paragraph that when missing creates an albino and a homozygous caramel would also have mistakes in both copies of it's volume B page 200 but it's mistake would be different, only the two switched letters.

So if you bred a homozygous albino to a homozygous caramel neither parent would have a normal copy of volume B page 200 to give to the babies.  Each baby would be a double het but since both mutations are on the same page neither baby would have a normal copy of that page and might well look part way in-between the two mutations.

So think of a locus as a certain page in a certain volume and alleles as different mistakes on the same volume and page as opposed to different mistakes on different volumes and pages (example albino and axanthic). You can use this analogy further to think of linking as different mutations on different pages that happen to be in the same volume.  It makes a difference because the parent tends to copy the same of it's two source volumes when making a single copy for its offspring and can only make the initial single volume combining the two linked mutations if it is a double het and switches the right way between copying from its two source chromosomes/volumes.  If the linked mutations are on pages very close together it might take a long time for a crossover to happen on the few pages in-between in order to create a single volume with both mistakes.

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