Tracing model generated DNA with position independent watermark verification

Generation time watermarks support provenance for generative models, but verifi- cation becomes a synchronization problem when token alignment is unknown. In genomic sequences, a verifier may lack strand orientation, token phase, generation boundaries, and the location of the generated region; insertions and deletions can further disrupt alignment. We introduce a position independent verification frame- work that searches both strands, every nucleotide start, and four window lengths. Under an explicit null model for keyed bits, a Bonferroni correction converts the strongest window statistic into one read level significance decision, accounting for the full search without assuming independence between overlapping windows. Verification requires only the observed DNA, a key, and public settings. We instan- tiate the framework with the existing SynthID tournament watermark in Carbon- 500M and GENERator-v2 1.2B under canonical six mer sampling. Across 192 held out prompts with two draws each, the verifier detected 384/384 correct key marked reads per model, both unedited and after each tested single nonadaptive substitution, insertion, or deletion. Each ordinary and wrong key control family yielded at most one positive among 384 reads per model and condition at a de- clared 1% threshold. Neither model showed a statistically detectable difference across 14 prespecified model likelihood and sequence measures after correction. These results support verification without model access under unknown synchro- nization in the evaluated six mer and single edit regime.