It has come to the attention of this author that recent versions of the BLASTN algorithm employed as a local installation may be omitting significant levels of query sequences in large-scale genomic searches. This claim potentially affects the results of past research done by this author, particularly in relation to human-chimp DNA similarity. Therefore, six different versions of the BLASTN algorithm (2.2.25+, 2.2.26+, 2.2.27+, 2.2.28+, 2.2.29+, 2.2.30+) were tested using chimpanzee genomic sequence queried against human in sequence sets of '10', '100', '1,000', '10,000' and '100,000' sequences of randomly obtained 300 base fragments derived from three different chimpanzee chromosomes (providing three experimental replications). Surprisingly, only BLASTN version 2.2.25+ returned hits for nearly all query sequences. Every later version of the algorithm omitted significant levels of query sequence with the problem generally increasing with progressive algorithm releases. Therefore, a previous study by this author (using v. 2.2.27+) in which chimpanzee chromosomes were compared to human was repeated using the 2.2.25+ version of the algorithm in addition to the use of two other DNA pairwise algorithms (LASTZ and nucmer). For both LASTZ and nucmer, alignments as low as 50% identity were allowed along with the inclusion of all repetitive sequence. The analyses with BLASTN v 2.2.25+ and nucmer indicate that the alignable portions of the current chimpanzee genome assembly are 88% similar on average to human. The LASTZ algorithm only returned an average overall similarity of 73%. Detailed results and issues associated with each analysis are discussed.