Genome editing using engineered nucleases such as transcription activator-like 
effector nucleases (TALENs) has become a powerful technology for reverse 
genetics. In this study, we have described efficient detection methods for 
TALEN-induced mutations at endogenous loci and presented guidelines of TALEN 
design for efficient targeted mutagenesis in medaka, Oryzias latipes. We 
performed a heteroduplex mobility assay (HMA) using an automated microchip 
electrophoresis system, which is a simple and high-throughput method for 
evaluation of in vivo activity of TALENs and for genotyping mutant fish of F1 or 
later generations. We found that a specific pattern of mutations is dominant for 
TALENs harboring several base pairs of homologous sequences in target sequence. 
Furthermore, we found that a 5' T, upstream of each TALEN-binding sequence, is 
not essential for genomic DNA cleavage. Our findings provide information that 
expands the potential of TALENs and other engineered nucleases as tools for 
targeted genome editing in a wide range of organisms, including medaka.