[BiO BB] Doubt regarding paiwise alignment

[A KUNTHAVAI]

Hai,
        I am working in pairwise local alignment . While comparing two sequences 
  first I have found all matches.To find the highest similarity I took the matching point as a starting point. I do not know where I  should stop. that is starting from the first match whether I have to search the string until last letter in any one of the sequence or is there any other condition to stop.
   
  A.Kunthavai

				
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