Contamination A query sequence containing one or more segments of foreign sequence is said to be contaminated because the foreign sequence does not represent the genetic information from the biological source organism. Judging the Significance of a Match Strong and Moderate Matches to Vector By definition, strong matches very rarely occur by chance and moderate matches rarely occur by chance. The occasional moderate match that occurs by chance will lack any corroborating evidence of contamination . Weak Matches to Vector Weak matches identify sequence segments that are potentially of foreign origin. Although weak matches often occur by chance, they indicate foreign sequence whenever there is corroborating evidence of contamination .
Foreign sequences are therefore much more commonly found near the ends of a query.
Occasionally, however, foreign DNA segments can be found in the middle of a query sequence. Internal matches should therefore be checked for the presence of cloning sites or other corroborating evidence that would support the conclusion that the segment is foreign. If no corroborating evidence is found, or if a large portion of the query sequence matches vector, or if the matching segment lies in an open reading frame or other critical region, see Exceptions for possible alternative explanations for the match. The location of potential cloning sites can be found by a restriction site analysis of the query sequence. The match is to an adapter, linker or PCR primer Even short matches to adapter, linker or PCR primer sequences are strong evidence that the segment has a foreign origin.