Methods for nucleic acid analysis

A method for screening for functional sequences in a genome of a first organism, comprising:

• providing a substrate having a plurality of detection probes, wherein each detection probe is at a known location, and wherein at least one of said detection probes is complementary to a known nucleic acid sequence in the genome from said first organism and at least one of said detection probes is non-complementary to a known nucleic acid sequence in the genome from said first organism;
• contacting at least one sample nucleic acid from a second organism with said substrate, where said second organism diverged evolutionarily from said first organism between about 60 million years ago and about 120 million years ago, and where said contacting is performed under conditions wherein when said at least one sample nucleic acid is substantially complementary to a detection probe said at least one sample nucleic acid will preferentially hybridize to a detection probe to which it is most complementary, resulting in at least one hybridized detection probe;
• determining a location of said at least one hybridized detection probe;
• and
• identifying sequences of said at least one hybridized detection probe by referring to the location of said at least one hybridized detection probe;
• wherein when said sequence of said at least one hybridized detection probe is the same as a sequence complementary to said known nucleic acid sequence from said first organism, there is sequence similarity between nucleic acids from said first organism and said second organism, and regions in said nucleic acids of said first organism where there is sequence similarity with said nucleic acids from said second organism are candidate functional regions in said nucleic acids of said first organism.