An ambiguity in molecule reconstruction is presented when substituting a fragment for another with multiple attachments of the same type. We developed an alignment fingerprint (afp) taking inspiration from RATS to compute an optimal alignment between query fragment and candidate replacement. The alignment aims to map the attachment ids of the query fragment to those of the replacement. All valid (query, replacement) mappings are enumerated and each potential alignment is scored according to the sum of Tanimoto similarities of environments of the mapped attachment points. Attachment point environments are encoded by a molecular path fingerprint with its root at the attachment point. The alignment score has a maximum value of n where n is the number of attachment points in both the query and candidate fragments, since each perfectly identical (query, replacement) attachment pair has a similarity score of 1.