A method for detecting the presence of a target sequence comprising: a. adding a probe, said probe having been produced by a method comprising: i. obtaining double strand polynucleotides known to contain complementary target sequences and repetitive sequences; ii. fragmenting said double strand polynucleotides into fragments; iii. denaturing said fragments into single strands; iv. hybridizing said repetitive sequences to form a mixture of double strands and single strands; v. cleaving said double strands; and vi. amplifying said single strands wherein said single strands are complementary to said target sequences; and b. detecting said probe wherein said detection is selected from a group consisting of ISH, FISH, CGH, spectral karyotyping, chromosome painting, Northern blots, Southern blots, microarray analysis, and combinations thereof.