DNA Sequence Lab

DNA sequence (SpCas9, 20 nt guide + NGG PAM, both strands)

DNA sequence (scan for internal Type IIS sites that break assembly)

Sequence A

Sequence B

Local alignment, match +2, mismatch −1, gap −2. Sequences capped at 120 nt.

Template DNA sequence

Product size min (bp)

Product size max (bp)

Primer3-style design, length 18–27 (opt 20), Tm 57–63 °C (opt 60), GC 40–60%, 3′ GC clamp. Nearest-neighbour Tm (SantaLucia, 50 mM Na⁺, 0.25 µM primer). Nothing is uploaded.

Which strand did you paste?

DNA sequence

RNA polymerase reads the template strand and builds an mRNA identical to the coding strand, with U in place of T. Paste either strand and pick which it is.

DNA sequence — IUPAC ambiguity codes (R, Y, N, W…) are accepted

Gives the reverse complement, plus the complement and reverse on their own, and the two strands paired as a duplex. Useful for turning a forward primer into its reverse, or reading a sequencing result off the other strand.