AptaRender

Drag a base: move its whole branch (the stem and everything it encloses).
Alt+drag: move just that one base.
Ctrl/⌘+drag: move just its part — the helix it's in, the loop ring, or the free end.
Ctrl/⌘+click: add that part to the selection. Shift+drag the background: box-select.
Dragging any selected base moves the whole selection.

1. Ctrl/⌘+click an unpaired base of a loop to select its ring.
2. Click Lock ring.
3. Drag any helix attached to the ring (or the rest of the molecule) to swing it around the ring. The ring keeps its size; its unpaired bases spread out between the helices.
Click Unlock or press Esc when done.

Click a base on the canvas to select it. Shift-click to add.

Enlarge or shrink just the selected bases (letter and circle together), relative to the font size above. The font-size slider still changes everything.

Upload a .txt with one line per position (or range): position [base] color [target], e.g. 12 G #e15554 or 5-9 orange circle. Download the sample to see the full format.

Click a base on the canvas to select it, then apply a fill.

Click a base-pair rung to select it. Shift-click to add. Unselected rungs use the global rung color.

none selected

A complex joins two of your sequences with a manually-set duplex region. Build one below, then open the Letters/Circles tabs to color each strand.

A[aStart..aEnd] pairs antiparallel with B[bStart..bEnd] — ranges must be equal length. Replace mode: any existing base pair that touches or spans the duplex region (in either strand) is broken, and the region becomes a fresh straight duplex. Side-by-side mode: strand A's own structure is left completely untouched (including pairs inside the chosen range) and B is laid out running parallel to it — the same A bases can end up with two drawn bonds (their own, plus the new one to B). This isn't biophysically possible for real base pairing, but the tool won't stop you — draw what communicates the figure you need. Exactly one contiguous region either way in this version.

Intramolecular H-bonds keep using the Lines tab's rung color / per-bond colors from each strand's own sequence. Individual duplex rungs aren't separately colorable in this version.

Leave blank to use the sequence's name. .svg / .png is added for you.

SVG stays fully editable in Illustrator/Inkscape — every base is its own text element. PNG dimensions shown above.