Mouse Breeding Planner

Plan crosses for genetically modified mouse lines. Enter your breeders and the mice you need to get genotype ratios, the number of litters and breeding cages, a timeline, and faster alternative crosses. Everything runs in your browser; nothing you enter is stored or sent anywhere.

Your breeders

List each allele in the cross (transgene, Cre, flox, knockout, reporter) and how many copies each breeder carries. Use + for wild type.

Allele 1 nameFemale breederMale breederX-linked

Allele 2 nameFemale breederMale breederX-linked

Mice you need

Describe each experimental group. Add littermate controls as their own group so the plan makes enough of both.

GroupCreflSexNumber needed

Your colony

Typical values for C57BL/6J mice are filled in. Change them to match your strain and facility.

Pups per litter% surviving to weaningAge at experiment (weeks)Pairing dateBreeding cagesConfidence of enough mice

Your plan

Experimental

50%

of pups (1 in 2) · about 2.5 per litter

Littermate controls

50%

of pups (1 in 2) · about 2.5 per litter

You need 7 litters for a 90% chance of getting every group. On average, 3.9 litters would be enough, but genotypes vary from litter to litter.

Breeding females	Pair cages	Litters each	All 8-week-old mice by
7	7	1	Jan 14, 2027 · first mice Jan 14, 2027
4	4	2	Feb 11, 2027 · first mice Jan 14, 2027
3	3	3	Mar 11, 2027 · first mice Jan 14, 2027

Dates assume the first litter about 3.5 weeks after pairing and a new litter every 4 weeks.

No other combination of breeder genotypes needs fewer litters for these groups.

All offspring genotypes

Percent of all pups. Sexes are 50:50 for every genotype.

Genotype	Pups	Group
+/+; fl/fl	50%	Littermate controls
Cre/+; fl/fl	50%	Experimental

How the numbers are calculated

Genotype ratios follow Mendelian inheritance. Each allele is assumed to be inherited independently (not linked on the same chromosome), sexes are 50:50, and every genotype survives equally. If two alleles sit close together on one chromosome, or a genotype is embryonic lethal, real ratios will differ.

For X-linked alleles, fathers pass their X chromosome to every daughter and to none of their sons, so the planner tracks offspring sex whenever an allele is marked X-linked.

Litters needed: the number of weaned pups per litter is modeled as a Poisson count with a mean of pups per litter × survival to weaning. The planner finds the smallest number of litters that gives every group enough mice with the confidence you choose. Real litter sizes vary a little less than this model assumes, so the estimate errs slightly on the safe side.

Before you breed, check the line’s notes from JAX or your supplier: some Cre lines show germline recombination and should be passed through one sex only, and some lines breed poorly as homozygotes.