AbstractThere is significance in the molecular weight derived sequence patterns of adenosine, guanosine, cytosine, thymine, methyl cytosine and hydroxyl methyl cytosine if one has to consider the molecular events holistically by including single nucleotide polymorphisms, tumor suppressor gene activity like that of ten eleven translocation gene, CpG methylation, miRNA SNP patterns and SNPs neighboring CpGs. This research article focuses on observing simulation results of validated SNPs in a sequence using substitution patterns of molecular weight of A, G, C, T, 5OHC, 5MC. The outcome helped to bring out positions in a DNA sequence where in validated bi allelic SNPs were never found to occur and SNPs neighboring methylated CpGs do show disconcordance and a simulated effect of gene function like that of ten eleven translocation do show disconcordance with other SNP occurrence patterns. Further the occurrence position of miRNA SNPs do differ from other SNPs. Hence molecular weight based recognition of sequences might play a role in genome evolution, cancer related methylation and variation.