1 0 0 ▁am ino ▁ac ids . ▁When ▁the ▁alignment ▁of ▁the ▁th ▁and ▁th ▁am ino ▁ac ids ▁is ▁considered , ▁the ▁score ▁indicates ▁the ▁relative ▁lik elihood s ▁of ▁the ▁alignment ▁due ▁to ▁the ▁prote ins ▁being ▁related ▁or ▁due ▁to ▁random ▁chance . ▁ ▁If ▁the ▁prote ins ▁are ▁related , ▁a ▁series ▁of ▁point ▁accepted ▁mut ations ▁must ▁have ▁occurred ▁to ▁mut ate ▁the ▁original ▁am ino ▁acid ▁into ▁its ▁replacement . ▁Suppose ▁the ▁th ▁am ino ▁acid ▁is ▁the ▁original . ▁Based ▁on ▁the ▁abund ance ▁of ▁am ino ▁ac ids ▁in ▁prote ins , ▁the ▁probability ▁of ▁the ▁th ▁am ino ▁acid ▁being ▁the ▁original ▁is ▁. ▁Given ▁any ▁particular ▁unit ▁of ▁this ▁am ino ▁acid , ▁the ▁probability ▁of ▁being ▁replaced ▁by ▁the ▁th ▁am ino ▁acid ▁in ▁the ▁assumed ▁time ▁interval ▁is ▁. ▁Thus , ▁the ▁probability ▁of ▁the ▁alignment ▁is ▁, ▁the ▁numer ator ▁within ▁the ▁log arith m . ▁ ▁If ▁the ▁prote ins ▁are ▁not ▁related , ▁the ▁events ▁that ▁the ▁two ▁aligned ▁am ino ▁ac ids ▁are ▁the ▁th ▁and ▁th ▁am ino ▁ac ids ▁must ▁be ▁independent . ▁The ▁prob abilities ▁of ▁these ▁events ▁are ▁ ▁and ▁, ▁which ▁means ▁the ▁probability ▁of ▁the ▁alignment ▁is ▁, ▁the ▁denomin ator ▁of ▁the ▁log arith m . ▁ ▁Thus , ▁the ▁log arith m ▁in ▁the ▁equation ▁results ▁in ▁a ▁positive ▁entry ▁if ▁the ▁alignment ▁is ▁more ▁likely ▁due ▁to ▁point ▁accepted ▁mut ations , ▁and ▁a ▁negative ▁entry ▁if