Abstract: Methods including in-silico steps for design and synthesis of Genomic Morse Code (“GMC”) probes including design of combinations of polynucleotide sequences and labelling colors for analysis of large rearrangements in targeted genetic regions as well as allele characterization of complex regions and localization of events such as replication, DNA reparation or epigenetics in particular regions. Color-encoded sets of probes that produce characteristic or unique color patterns when painted on a target nucleic acid sequence. Methods for using color-encoded sets of probes.