The numbers in italics on the diagonal are the corrected pairwise sequence differences (changes per 100 bp) between the common parts of the left and right LTRs (209-bp alignment). All other numbers are the corrected pairwise differences between alleles, using assembled sequences that contain the flanks of each allele out to the PCR primer binding sites plus each of the LTRs (903-bp alignment). The allele names shown in the top row give the species from which the allele was obtained (first three letters), a designation in capital letters of either the allele (Y or Z) or the location from which the mouse was obtained (MX, Mexico; CA, California; IA, Iowa; ME, Maine; GA, Georgia; MA, Massachusetts; TX, Texas; CT, Connecticut), and the size of the amplified allele in kilobases (e.g., 3.78). The criY3.78 and criZ3.78 alleles came from the same individual, as did the manIA4.10 and manIA3.75 alleles. GenBank accession nos. for the sequences in the order shown in this table are AY017268–AY017293. There are two accession numbers assigned to each allele, the first for the left flank and left LTR, the second for the right LTR and right flank.