Abstract: Provided in certain aspects are methods for dynamically adding molecular indexes to nucleic acid, and optionally analyzing the tagged nucleic acid. Also provided in certain aspects are methods for producing a single-stranded nucleic acid molecule from two molecules. The first molecule typically is a single-stranded nucleic acid (ssNA) containing a target sequence with optional linked nucleic acid sequences. The second molecule typically is a ssNA containing a target binding sequence and a nucleic acid sequence “tag” that is not complementary to the target sequence.