Tools shRNA and CRISPR Design shRNA Target Design Design optimal shRNA sequences by knockdown score and position for your target sequence. Sequence Analysis Sequence Alignment Pair-wise comparison of DNA, protein, or translation-based DNA sequences. Sequence Dot Plot Two-dimensional plot for identifying regions with similar features between two DNA or RNA sequences. GC Content Calculator Calculate GC content of entire sequence and specific regions. DNA Secondary Structure Predict secondary structures from base pair interactions. DNA Reverse Complement Retrieve reverse, complement, or reverse complement sequences. Sequence Optimization Analysis Codon Optimization Optimize codons according to species, cleavage sites, and clonability. DNA Translation Retrieve amino acid sequence from DNA input.