ArrayPlot[ Table[StringLength@ LongestCommonSequence[StringTake[#[[1]] 1, i], StringTake[#[[2]], j]], {i, 1, StringLength[#[[1]]], 1}, {j, 1, StringLength[#[[2]]], 1}], ColorFunction -> "RedBlueTones"] &@ Table[StringJoin[RandomChoice[{"A", "C", "T", "G"}, 80]], {2}]