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MAVisto
MAVisto 2.7.0   
MAVisto is a tool for the exploration of motifs in network. It provides a flexible motif search algorithm and different views for the analysis and visualisation of network motifs. MAVisto is written ...
Freeware

Primer Premier
Primer Premier 6.25   
... homology among multiple candidate oligos. Restriction enzyme and motif analysis- Select from the database of over 800 enzymes and 200 common motifs. Clustal W alignments- Load the aligned sequences after
Demo
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