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}]